Bbs4 (Bardet-Biedl syndrome 4) - Rat Genome Database

Name: Bbs4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Bbs4 (Bardet-Biedl syndrome 4) Rattus norvegicus

Analyze

Symbol:

Bbs4

Name:

Bardet-Biedl syndrome 4

RGD ID:

1309134

Description:

Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity; cytoskeletal protein binding activity; and protein-macromolecule adaptor activity. Involved in protein localization to centrosome. Predicted to be located in several cellular components, including ciliary membrane; microtubule organizing center; and photoreceptor cell cilium. Predicted to be part of BBSome. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome 4; morbid obesity; and obesity. Orthologous to human BBS4 (Bardet-Biedl syndrome 4); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 2,4-dinitrotoluene; acrylamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Bardet-Biedl syndrome 4 homolog; Bardet-Biedl syndrome 4 homolog (human) ; LOC300754

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	BBS4 (Bardet-Biedl syndrome 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Bbs4 (Bardet-Biedl syndrome 4 (human))	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Bbs4 (Bardet-Biedl syndrome 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	BBS4 (Bardet-Biedl syndrome 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Bbs4 (Bardet-Biedl syndrome 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	BBS4 (Bardet-Biedl syndrome 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	BBS4 (Bardet-Biedl syndrome 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Bbs4 (Bardet-Biedl syndrome 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	BBS4 (Bardet-Biedl syndrome 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Bbs4 (Bardet-Biedl syndrome 4 (human))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	bbs4 (Bardet-Biedl syndrome 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	BBS4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	bbs-4	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	59,731,912 - 59,765,408 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	8	59,731,912 - 59,765,607 (-)	Ensembl
Rnor_6.0	8	64,115,005 - 64,154,432 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	64,121,392 - 64,154,396 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	63,883,342 - 63,916,346 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	63,153,456 - 63,189,904 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	63,173,427 - 63,210,255 (-)	NCBI
Celera	8	59,173,803 - 59,207,298 (-)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bardet-Biedl syndrome (ISO)

Bardet-Biedl syndrome 1 (ISO)

Bardet-Biedl syndrome 4 (ISO)

Bloom syndrome (ISO)

Brugada syndrome 8 (ISO)

colon cancer (ISO)

fundus dystrophy (ISO)

intellectual disability (ISO)

morbid obesity (ISO)

obesity (ISO,ISS)

retinal degeneration (ISO)

retinitis pigmentosa (ISO)

schizophrenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

1,2-dimethylhydrazine (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

2,2',5,5'-tetrachlorobiphenyl (EXP)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-dinitrotoluene (EXP)

4-hydroxyphenyl retinamide (ISO)

5-fluorouracil (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

C60 fullerene (EXP)

carbon nanotube (ISO)

choline (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

cyclophosphamide (ISO)

cyclosporin A (ISO)

decabromodiphenyl ether (EXP)

dicrotophos (ISO)

disodium selenite (ISO)

doxorubicin (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

L-methionine (ISO)

leflunomide (ISO)

methyl methanesulfonate (ISO)

paclitaxel (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

potassium dichromate (ISO)

quercetin (ISO)

Soman (EXP)

testosterone (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adult behavior (ISO)

biological_process (ND)

brain morphogenesis (ISO)

centrosome cycle (ISO)

cerebral cortex development (ISO)

cilium assembly (IBA,ISO)

dendrite development (ISO)

face development (ISO)

fat cell differentiation (ISO)

fat pad development (ISO)

hippocampus development (ISO)

leptin-mediated signaling pathway (ISO)

maintenance of protein location in nucleus (ISO)

microtubule anchoring at centrosome (ISO)

microtubule cytoskeleton organization (ISO)

mitotic cytokinesis (ISO)

negative regulation of actin filament polymerization (ISO)

negative regulation of appetite by leptin-mediated signaling pathway (ISO)

negative regulation of gene expression (ISO)

negative regulation of GTPase activity (ISO)

negative regulation of systemic arterial blood pressure (ISO)

neural tube closure (ISO)

neuron migration (ISO)

non-motile cilium assembly (ISO)

photoreceptor cell maintenance (ISO)

photoreceptor cell outer segment organization (ISO)

positive regulation of cilium assembly (ISO)

positive regulation of multicellular organism growth (ISO)

protein localization (ISO)

protein localization to centrosome (IGI,IMP,ISO)

protein localization to cilium (IBA,ISO)

protein localization to organelle (ISO)

protein localization to photoreceptor outer segment (ISO)

regulation of cilium beat frequency involved in ciliary motility (ISO)

regulation of cytokinesis (ISO)

regulation of lipid metabolic process (ISO)

regulation of non-motile cilium assembly (ISO)

regulation of stress fiber assembly (ISO)

response to leptin (ISO)

retina homeostasis (ISO)

retinal rod cell development (ISO)

sensory perception of smell (ISO)

social behavior (ISO)

spermatid development (ISO)

striatum development (ISO)

ventricular system development (ISO)

Cellular Component

BBSome (ISO)

cellular_component (ND)

centriolar satellite (ISO)

centriole (ISO)

centrosome (ISO)

ciliary basal body (ISO)

ciliary membrane (ISO)

ciliary transition zone (ISO)

cilium (ISO)

cytosol (IEA,ISO)

membrane (ISO)

motile cilium (ISO)

non-motile cilium (ISO)

nucleus (IEA)

pericentriolar material (ISO)

photoreceptor connecting cilium (ISO)

photoreceptor inner segment (ISO)

photoreceptor outer segment (ISO)

Molecular Function

alpha-tubulin binding (ISO)

beta-tubulin binding (ISO)

dynactin binding (ISO)

molecular_function (ND)

protein binding (ISO)

protein-macromolecule adaptor activity (ISO)

RNA polymerase II-specific DNA-binding transcription factor binding (ISO)

References

References - curated


1.	Benzinou M, etal., Diabetes. 2006 Oct;55(10):2876-82.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Kamiya A, etal., Arch Gen Psychiatry. 2008 Sep;65(9):996-1006. doi: 10.1001/archpsyc.65.9.996.
4.	Kim JC, etal., Nat Genet. 2004 May;36(5):462-70. Epub 2004 Apr 25.
5.	MGD data from the GO Consortium
6.	OMIM Disease Annotation Pipeline
7.	RGD automated data pipeline
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions
10.	RGD comprehensive gene curation
11.	Zhang Y, etal., Hum Mol Genet. 2014 Jan 1;23(1):40-51. doi: 10.1093/hmg/ddt394. Epub 2013 Aug 13.

Additional References at PubMed

PMID:14520415	PMID:15173597	PMID:15322545	PMID:15539463	PMID:15649943	PMID:16170314	PMID:16794820	PMID:17379567	PMID:17519557	PMID:17574030	PMID:17591906	PMID:18022666
PMID:18032602	PMID:18299575	PMID:18317593	PMID:18334641	PMID:18443298	PMID:19150989	PMID:20080638	PMID:20398886	PMID:21444805	PMID:22072986	PMID:22139371	PMID:22228099
PMID:22302990	PMID:22500027	PMID:23178122	PMID:23716571	PMID:24469809	PMID:24550735	PMID:24695551	PMID:27979967

Genomics

Comparative Map Data

Bbs4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	59,731,912 - 59,765,408 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	8	59,731,912 - 59,765,607 (-)	Ensembl
Rnor_6.0	8	64,115,005 - 64,154,432 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	64,121,392 - 64,154,396 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	63,883,342 - 63,916,346 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	63,153,456 - 63,189,904 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	63,173,427 - 63,210,255 (-)	NCBI
Celera	8	59,173,803 - 59,207,298 (-)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

BBS4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	72,686,179 - 72,738,475 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	72,686,204 - 72,738,476 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	72,978,548 - 73,030,814 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	70,765,588 - 70,817,869 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	70,765,587 - 70,817,869	NCBI
Celera	15	49,857,583 - 49,909,622 (+)	NCBI
Cytogenetic Map	15	q24.1	NCBI
HuRef	15	49,809,136 - 49,861,119 (+)	NCBI		HuRef
CHM1_1	15	73,096,698 - 73,148,926 (+)	NCBI		CHM1_1

Bbs4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	59,229,249 - 59,260,791 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	9	59,229,273 - 59,260,791 (-)	Ensembl
GRCm38	9	59,321,966 - 59,353,508 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	59,321,990 - 59,353,508 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	59,169,773 - 59,201,315 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	9	59,119,972 - 59,151,466 (-)	NCBI			mm8
Celera	9	56,549,258 - 56,580,867 (-)	NCBI		Celera
Cytogenetic Map	9	B	NCBI
cM Map	9	32.01	NCBI

Bbs4
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955450	4,631,266 - 4,662,719 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955450	4,624,634 - 4,668,470 (-)	NCBI	ChiLan1.0	ChiLan1.0

BBS4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	15	70,362,007 - 70,416,964 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	70,362,261 - 70,416,964 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	51,601,526 - 51,656,460 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

Bbs4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	114,114,361 - 114,171,453 (+)	NCBI
SpeTri2.0	NW_004936471	31,962,500 - 32,019,516 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

BBS4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	7	60,631,913 - 60,693,359 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	65,150,187 - 65,267,538 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

BBS4
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	26	10,742,982 - 10,799,615 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	26	10,743,850 - 10,775,908 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666048	130,788,533 - 130,854,411 (+)	NCBI	Vero_WHO_p1.0

Bbs4
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624781	1,502,069 - 1,553,101 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH136649

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	8	59,733,616 - 59,733,810 (+)	MAPPER	mRatBN7.2
Rnor_6.0	8	64,123,097 - 64,123,290	NCBI	Rnor6.0
Rnor_5.0	8	63,885,047 - 63,885,240	UniSTS	Rnor5.0
RGSC_v3.4	8	63,155,161 - 63,155,354	UniSTS	RGSC3.4
Celera	8	59,175,508 - 59,175,701	UniSTS
RH 3.4 Map	8	702.09	UniSTS
Cytogenetic Map	8	q24	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	8462195	110921472	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10378157	112202585	Rat
1558646	Swd5	Spike wave discharge measurement QTL 5	3.45	0.00036	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	8	14906751	59906751	Rat
61373	Mcs4	Mammary carcinoma susceptibility QTL 4	1.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	8	16290444	61290444	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	18984168	84531599	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	19331152	93965294	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	22662330	67662330	Rat
2303564	Gluco43	Glucose level QTL 43	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	26130187	71130187	Rat
2303572	Insul13	Insulin level QTL 13	2		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	8	26130187	71130187	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	27205715	99103503	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	27205715	99103503	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	27205715	99103503	Rat
1300146	Rf17	Renal function QTL 17	2.9		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	8	28242912	73242912	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	28242912	99525068	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	29502665	70386295	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	30188867	94457446	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	61290444	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	61290444	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	30848154	61290444	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	30848154	61290444	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	30848154	61290444	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	61290444	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	30848154	82460899	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	30848154	82460899	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	30848154	82460899	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	30848154	82460899	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	30848154	101699754	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	30848154	101699754	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	30848154	101699754	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	30848259	105647037	Rat
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	30856404	75856404	Rat
1582222	Epfw2	Epididymal fat weight QTL 2	3.2	0.0005	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	8	31737729	76737729	Rat
61358	Bp39	Blood pressure QTL 39	2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	35551938	80551938	Rat
61464	Niddm11	Non-insulin dependent diabetes mellitus QTL 11	3.1	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	35582032	80582032	Rat
1331838	Niddm61	Non-insulin dependent diabetes mellitus QTL 61	3.53	0.0004	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	36469535	99083736	Rat
737824	Hcar10	Hepatocarcinoma resistance QTL 10	2.9		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	8	40713066	82925667	Rat
1358906	Bp253	Blood pressure QTL 253	4	0.0004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	40713066	93965294	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	40952565	123900184	Rat
1331769	Rf39	Renal function QTL 39	3.871		urine output (VT:0003620)	timed urine volume (CMO:0000260)	8	41866876	75097878	Rat
1298079	Activ2	Activity QTL 2	9.5	0.000001	voluntary movement trait (VT:0003491)	rearing measurement (CMO:0001515)	8	41866876	86866876	Rat
631216	Stl9	Serum triglyceride level QTL 9	4.71	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	8	41867010	70386132	Rat
70161	Bp62	Blood pressure QTL 62	2.9	0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	42692684	90165460	Rat
12879882	Am8	Aortic mass QTL 8		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	43296169	98968765	Rat
12879878	Bw183	Body weight QTL 183		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	43296169	98968765	Rat
12879879	Cm99	Cardiac mass QTL 99		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	43296169	98968765	Rat
12879880	Cm100	Cardiac mass QTL 100		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	43296169	98968765	Rat
12879881	Cm101	Cardiac mass QTL 101		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	8	43296169	98968765	Rat
12879883	Kidm65	Kidney mass QTL 65		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	43296169	98968765	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	46531639	119088624	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	8	46531639	119088624	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	8	46531639	119088624	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	46531639	119088624	Rat
1331837	Bw23	Body weight QTL 23	4.19	0.00007	body mass (VT:0001259)	body weight (CMO:0000012)	8	46531722	99083736	Rat
2303570	Gluco48	Glucose level QTL 48	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	49805831	94805831	Rat
2313086	Bss60	Bone structure and strength QTL 60	4.1	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	8	50095249	82460899	Rat
4889938	Bss89	Bone structure and strength QTL 89	3.8		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	8	50095249	82460899	Rat
5684973	Bss100	Bone structure and strength QTL 100	4.7		tibia area (VT:1000281)	tibia area measurement (CMO:0001382)	8	50095249	82460899	Rat
1358912	Bw51	Body weight QTL 51	2.95		body mass (VT:0001259)	body weight (CMO:0000012)	8	51351728	107062046	Rat
10402857	Bp380	Blood pressure QTL 380		0.95	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	53968765	98968765	Rat
2301402	Bp316	Blood pressure QTL 316		0.005	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	53968765	98968765	Rat
2293697	Bmd39	Bone mineral density QTL 39			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	8	54043744	98968765	Rat
1582243	Bw66	Body weight QTL 66	3.4	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	8	54237644	85365202	Rat
1582254	Kidm31	Kidney mass QTL 31	3		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	8	54237644	85365202	Rat
631664	Hcar3	Hepatocarcinoma resistance QTL 3	2.9	0.0005	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	8	54237644	99103503	Rat
1300177	Cm2	Cardiac mass QTL 2	3.65		heart mass (VT:0007028)	heart weight (CMO:0000017)	8	54259986	100382532	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	118
Count of miRNA genes:	90
Interacting mature miRNAs:	106
Transcripts:	ENSRNOT00000031262
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	28	26	10	19	10	1	1	74	34	40	11	1
Low		15	31	31		31	7	10		1	1		7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106826	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008766225	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008766226	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017595558	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017595559	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017595560	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081094	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081095	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000198	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000031262 ⟹ ENSRNOP00000030021

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	8	59,731,912 - 59,765,408 (-)	Ensembl
Rnor_6.0 Ensembl	8	64,121,392 - 64,154,396 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000104326 ⟹ ENSRNOP00000092159

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	8	59,731,912 - 59,765,607 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000110213 ⟹ ENSRNOP00000078115

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	8	59,731,912 - 59,761,951 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000119362 ⟹ ENSRNOP00000087657

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	8	59,731,912 - 59,761,951 (-)	Ensembl

RefSeq Acc Id:

NM_001106826 ⟹ NP_001100296

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	59,731,912 - 59,765,408 (-)	NCBI
Rnor_6.0	8	64,121,392 - 64,154,396 (-)	NCBI
Rnor_5.0	8	63,883,342 - 63,916,346 (-)	NCBI
RGSC_v3.4	8	63,153,456 - 63,189,904 (-)	RGD
Celera	8	59,173,803 - 59,207,298 (-)	RGD

Sequence:

show sequence

CCGGTTTCGAGGCGGTGGGCGGAGCCAAGATGGCTGAGGAGAAGCTTGGGATGAAAACTCAGGT
TCCTGCATCTATTGAATCTCAAAAACCCAGGCCAAAAAAAGCTCCAGAGTTTCCTATTGTGGAG
AAGCTGAACTGGCTGATCCATCTCTACTATATCCGGAAGGATTATGAGGCGTGCAAGGCTGTGA
TCAAAGAACAGCTTCAGGAGACTCAAGGGCTGTGTGAATATGCTATTTATGTCCAAGCACTGAT
TTTCCGCCTGGAAGGAAATATCCAAGAATCCCTAGAACTCTTTCAGACGTGTGCTGTTCTCAGC
CCACAGTGTGCTGATAATCTCAAGCAGGTGGCCAGATCTTTATTTCTTCTGGGAAAACATAAAG
CCGCCACAGAAGTATATAATGAAGCAGCTAAGCTCAACCAGAAAGACTGGGAGATCTGCCATAA
CCTGGGAGTGTGCTACACTTACCTAAAGCAGTTCAGCAAGGCGCAAGACCAATTGCACAGTGCC
CTCCAGCTTAACAAGCATGACCTGACTTACATTATGCTGGGGAAGATCCATTTACTGCAGGGAG
ACTTGGATAAAGCCATTGAGATCTACAAGAAAGCAGTGGAGTTCTCTCCAGAAAATACAGAACT
TCTCACAACTTTAGGATTACTCTACCTACAGCTTGGTGTTTACCAGAAGGCATTTGAACACCTT
GGGAATGCACTGACTTACGACCCTGCCAACTACAAGGCCATCTTGGCAGCAGGCAGCATGATGC
AGACTCATGGGGACTTTGATGTTGCCCTTACCAAATACAGAGTTGTAGCTTGTGCTATTCCAGA
AAGTCCTCCACTTTGGAATAACATTGGAATGTGTTTCTTTGGCAAGAAGAAATACGTGGCAGCT
ATCAGCTGCCTAAAACGAGCCAATTACTTGGCACCCTTCGACTGGAAGATTCTGTACAATCTGG
GCCTTGTCCATTTGACCATGCAGCAGTATGCATCGGCATTCCACTTTCTCAGCGCAGCCATCAA
CTTCCAGCCAAAGATGGGGGAACTCTACATGCTCTTGGCTGTGGCTCTGACCAACCTGGAAGAC
ATAGAAAATGCCAAAAGAGCTTATGTAGAAGCTGTCCGCCTGGATAAGTGCAACCCTTTAGTAA
ACCTGAACTACGCTGTGCTGCTGTACAACCAGGGTGAGAAGAAGGGTGCCTTGGCTCAGTACCA
GGAGATGGAGAAGAAGGTCCATTTTCTCAAGGACAACAATCCTCTGGAATTTGATTCTGAGATG
GTAGAGATGGCTCAGAAGTTGGGAGCTGCCCTCCAGGTTGGAGAGGCACTGGTCTGGACCAAGC
CAGTCAAAGATCCCAAGTCAAAGCACCGGACCAATTCAGGCAGCAAATCTGCTACTCTCCAGCA
GCCTCTGGGCTCCTTTCAAGCTCTTGGACAGGCGATGTCTTCGGCAGCTGCACACAGGAAGATC
CCTTCAGGTGCTGTAGGAGCCCAGCTCACAAAGCCGCCATCACTTCCACTGGAGCCAGAGCCAG
AGCCCACTGTGGAGGCGAGTCCAACAGAAGCATCAGAACAAAACAAAGAAAAATAGCAACAAAC
ATGAAAATCCAGGATGACCCTGGAGTAGGGGGTGTCTCTTAAGTGAGACCATATAGAAGGTGGT
CACATGACCAAGCAGATGGAGGCCAACACTTCCTCCCTGGGTGGGCAGTGCAGAATAAAACAGA
ACCCAGGGTGTGTTGTGATGATCAGGAGGAGCCCAAGCAGCTCTTGGCTGGCCCCATCATAGGA
ACAAGGGAGAAGACATGCTACATAGACTTGAGGTCCTGCATGTATACTCCAAGACTCAGCAAGG
CAAATGATGAAAGACCATTACTCAGTGAAGGACTTTATCTTGATAACGGGAAAAGTACTCTACT
CAGTAGGCTGTGGTGATGAAGCTTCTTCATTCTAACTGGACTGTGGGAAGACGTAAGTCTCCAC
TGGAAACAAACCTTGGATTAAGAACCTAGTTAAATACGGCTTCCCCAACCACCACCACCACCAC
CACAACCACCACCACCACCACCACCCCTTTTAGATTAAGTTGAGATCCAAACTGGAATGAATCC
AGCTATATCTGCCCAAAGACAATCTAAAACAAGTCCTTATCTCCATTCTTCAGAGAGGTCAGAG
TCTAGAGCCAGATCATGTCAGTTTAAGTAGAGTCAAGGACTGGTCAGGAATTGGCGCCAAGAAT
TTAAAGAAAAAAGTGGGTAGGGTGACTGAGGACATAGCTCAGTATCAGAGCACTTGCTTAGCAT
ACACAAGGCCCTGGGTTTAATCCCCAGTACTGATGAAAAAGAACAGAGCTTTTCGATAAGGAAT
TTTAACCAAGACAATCAATGATGAATGCTGACAGATGCTCTCATGGCCCATTAGCAGCCTTTGT
GAAAGATTATGGATCTCCAAGAGGTCACATTAAAATATTTTTAAAAAAATAAAACTATGATCAC
TGTCTGTTTTTACC

hide sequence

RefSeq Acc Id:

XM_008766226 ⟹ XP_008764448

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	59,731,936 - 59,743,440 (-)	NCBI
Rnor_6.0	8	64,115,005 - 64,132,902 (-)	NCBI

Sequence:

show sequence

GTCCCCAGCTCCGAAAAAAAAAACAAAAACAAAAACAACAAAGAAACACACACACATACCCTTA
AGGTATCCATGACCATAAGAACCATCTTATGCTTTGATAACAACTGATTTTTGTTTGTTTTGGT
TGGTTTTTGAGACAGGGTTTCTCTGTGTAGCTCTGGCTGTCCTGGAACTCACTCTGAGACCAGG
CTGGCCTCAAACTCAGAGATCCACCTGCCTCTGGAGTGCTTGGATTAAAGGGGTGAGCCACCAT
ACCTGGCCTTCAGTTTTGCTTTTAAGGCGCAAGACCAATTGCACAGTGCCCTCCAGCTTAACAA
GCATGACCTGACTTACATTATGCTGGGGAAGATCCATTTACTGCAGGGAGACTTGGATAAAGCC
ATTGAGATCTACAAGAAAGCAGTGGAGTTCTCTCCAGAAAATACAGAACTTCTCACAACTTTAG
GATTACTCTACCTACAGCTTGGTGTTTACCAGAAGGCATTTGAACACCTTGGGAATGCACTGAC
TTACGACCCTGCCAACTACAAGGCCATCTTGGCAGCAGGCAGCATGATGCAGACTCATGGGGAC
TTTGATGTTGCCCTTACCAAATACAGAGTTGTAGCTTGTGCTATTCCAGAAAGTCCTCCACTTT
GGAATAACATTGGAATGTGTTTCTTTGGCAAGAAGAAATACGTGGCAGCTATCAGCTGCCTAAA
ACGAGCCAATTACTTGGCACCCTTCGACTGGAAGATTCTGTACAATCTGGGCCTTGTCCATTTG
ACCATGCAGCAGTATGCATCGGCATTCCACTTTCTCAGCGCAGCCATCAACTTCCAGCCAAAGA
TGGGGGAACTCTACATGCTCTTGGCTGTGGCTCTGACCAACCTGGAAGACATAGAAAATGCCAA
AAGAGCTTATGTAGAAGCTGTCCGCCTGGATAAGTGCAACCCTTTAGTAAACCTGAACTACGCT
GTGCTGCTGTACAACCAGGGTGAGAAGAAGGGTGCCTTGGCTCAGTACCAGGAGATGGAGAAGA
AGGTCCATTTTCTCAAGGACAACAATCCTCTGGAATTTGATTCTGAGATGGTAGAGATGGCTCA
GAAGTTGGGAGCTGCCCTCCAGGTTGGAGAGGCACTGGTCTGGACCAAGCCAGTCAAAGATCCC
AAGTCAAAGCACCGGACCAATTCAGGCAGCAAATCTGCTACTCTCCAGCAGCCTCTGGGCTCCT
TTCAAGCTCTTGGACAGGCGATGTCTTCGGCAGCTGCACACAGGAAGATCCCTTCAGGTGCTGT
AGGAGCCCAGCTCACAAAGCCGCCATCACTTCCACTGGAGCCAGAGCCAGAGCCCACTGTGGAG
GCGAGTCCAACAGAAGCATCAGAACAAAACAAAGAAAAATAGCAACAAACATGAAAATCCAGGA
TGACCCTGGAGTAGGGGGTGTCTCTTAAGTGAGACCATATAGAAGGTGGTCACATGACCAAGCA
GATGGAGGCCAACACTTCCTCCCTGGGTGGGCAGTGCAGAATAAAACAGAACCCAGGGTGTGTT
GTGATGATCAGGAGGAGCCCAAGCAGCTCTTGGCTGGCCCCATCATAGGAACAAGGGAGAAGAC
ATGCTACATAGACTTGAGGTCCTGCATGTATACTCCAAGACTCAGCAAGGCAAATGATGAAAGA
CCATTACTCAGTGAAGGACTTTATCTTGATAACGGGAAAAGTACTCTACTCAGTAGGCTGTGGT
GATGAAGCTTCTTCATTCTAACTGGACTGTGGGAAGACGTAAGTCTCCACTGGAAACAAACCTT
GGATTAAGAACCTAGTTAAATACGGCTTCCCCAACCACCACCACCACCACCACAACCACCACCA
CCACCACCACCCCTTTTAGATTAAGTTGAGATCCAAACTGGAATGAATCCAGCTATATCTGCCC
AAAGACAATCTAAAACAAGTCCTTATCTCCATTCTTCAGAGAGGTCAGAGTCTAGAGCCAGATC
ATGTCAGTTTAAGTAGAGTCAAGGACTGGTCAGGAATTGGCGCCAAGAATTTAAAGAAAAAAGT
GGGTAGGGTGACTGAGGACATAGCTCAGTATCAGAGCACTTGCTTAGCATACACAAGGCCCTGG
GTTTAATCCCCAGTACTGATGAAAAAGAACAGAGCTTTTCGATAAGGAATTTTAACCAAGACAA
TCAATGATGAATGCTGACAGATGCTCTCATGGCCCATTAGCAGCCTTTGTGAAAGATTATGGAT
CTCCAAGAGGTCACATTAAAATATTTTTAAAAAAATAAAACTATGATCACTGTCTGTTTTTACC
TATTTCTGAGCCTGGTTTGAAACTATTACCACCTCAAAGCCATGTTGCTCTTGGCTGTAGTGCA
GCCGCACAGCAGTGTAGAGGTCGGCCTCCTCTGAGGTAGGTCCAGTTGTTGTATAAGTGGCAGC
TACAGAACTGACACACGATCACGCCAGTGTGGAGACTGATACTTCAGCTGGGTCTGATGCGGCA
GACTGAACAGAGGTCCTCTTCTGTCCTCTAACCGGTGAAGGCAAGTACAGTACCAGAGGTGATG
CCTCGCCTGGGTAGCAGGTCTGCCATGCAGCAGTGGAGAAAACCTCTACGTCAGCATGGAGGGC
GGTATAGACTAAACTGACTTACAGAAACTAAAAGGTCTCGATGAGAGGTAAGAATGTAAGCTTC
TAAGAGGAGAAAGAAAACCAGGCCCTGAATCACCAGAAAGGAGGGTCTGCTTGCTTATAAGTGG
CAAATGAGAAGAGACTATATAGGGTAAATACTCATTCTGGACTTAAGACTAGAAATCTGGGTGA
CTAGGATCAATGACTTTTCAAGCCTGTTTGTAGGCATGTCTCTGAGATAATCCAATGATCTTAC
TAGACACCTAACTAACCTGACTTGGGGAGCAAAGTCTGTTTGAAGGGTCTGCTAGAGCACTGTT
CTTATCCTTTGGGGATCACACATCAGGTGTCCTGCATATCAGATATTTGTAAGTCATAATAGTA
CAGTCATAAAGTAGCAATGAAATAATTTTATGGTTGAGGTTATCACAACATGAAGAAGTGTATT
AAAAGGTTGCAGCATTAGGAAGGCTGAAAACCTCTGTGCTAGAGGAATCTGGATTCAGCGAAAG
CTAAAAAGTACAGGCTTAGGAAGTCGCAGAGATGGAAGGAAAACAGTGTTTAAGGAGAAAAGCG
GCATGGTGTTAAGGAAGGGAGGTCAGCCTTGGGAGTTTACCACAAAGTTACTGTCAGAAAGACC
AAGTCTACTGGGGAGGAACCTGCAGTTGGAGGAGAAAACCTGTTTTAGAAGGTACATGTCAGGC
TGCACTGGATTCGAACCTGGGGCTCAGTCCAGCCCCTATCCATCATGAAGCAGGACGCCCCCTT
GGAGAGCATGGTGGTGGTAGATGTCCATGCAGAGATTAAGCTGCTCATTTCACAAAGCTTCAGA
GGAGAGGAGGGATCTCTGAGGACAGAACTGAACTCCACGCTCCGAGATGACTTTACATGTTTGG
TTTTGAGACAGGGTCTCATGTATGGCTGGCTTCACACAGTGTAGCTGAGAGAATTTACTCCTGA
TAGCTTACTTCTACCTCTAAAGGCTGTTCTGGCTAAAATCTTAACATGGGGGTATACAAGTGCA
AAGGTGCTTTTCTCCTCGGTGAGGTATGGCAGAAACCGAGAGGCCTGTTCATTTTCTCCTGTTC
CTCGGGGGCAGTAGGGTACCTTTCTTTCACAAATAGTCACAAGCAACACTTTCTATAGTACCTG
GACTTAGGTTTTCTTAGATAACAGGCCATACATGTCATACATATCCAGTCTTCTGAGCATCTGG
TTTTGCAGTTTCTCATTCATTCTAAAAAGAATAAAAAGTTATTTTATGAAGGCAGCTCACAAGA
CAATTTTAAAGATTTAGGAAAATGAGACCAAATTGATAATCACAGAAACAATTCTGACCCATTA
ACAAGACTGAAACTAAGAACACTGCCAATACTATTAGCAGGGGTGCGGCACAGGTGCCTTGGAA
CTAAATTTTGCAGATTCCTTTTAAAAAAAATACTAAACATACTTTTATCTAATCCAAGAGTCAT
ACTAAAGTATTTGCCAGAATGAATTGGAAGCAATCACATAATCCCTTACACAGATGCCCAAACT
AGGAAGCAATCACGATATCTGTTTACGAGTGGATGAATAAACTTCAATGGAATCAGACAAAAGG
AAAAGTGCAAAAAGAAGCTATCAAGCTGAGAAAATGTATTATATTAAGTGAAAAATGCCAGTTT
AAAATACCCACATGATCTTAATATTGTATTCTGAAAATCTAGCCATTCTACAATGTTCTACTTT
GTTATCTAAAATTATTTTTTTATCAGTAAAGAAATAAATATGGCGTCAGGATACCACTGTGCAC
AGGAGTAAGTCGAACTGATTACAGACCTGACTGTCAAAGCCGAGTTCACACAGCTCCGAGAGAA
TCTGAGCCTGCATGATGATGTGCCATTTTGTTTCCTGGGTGCCGGGATCTGAACTTGTGTGGGG
CCCTCATGACTGCATTCTTCAGCCACTGGATCTGGCAACTGTTACAAGCCCATCTATTAGCAAA
GACTTGGATGCTGGGTCTGGGGCTTTAGGCCAAGCTTGCCCTTTAATAATTCTCAAGGGCTACT
CGCCTAGATCCAGAAGAGGATATCACTGACCATGCCCACATCAGGAACGCCATCCCAAGAGGAG
AGAGAAGCATGGGGTCCAGATGCTGACTGGCTGAGAAACAGCAGCTCCTGTTCATTCAGCCCAA
GAGAAGCCACTGCGGGAAAGACCTGCTAACAGAAATAATGACAGGTCTTTTTTGGGTGGACACA
GCTTCGCTCCTTGTGCATTAGGATACAGCCAATGACTAGAGGTCAGGCAGGCGTCTCTGAAACT
AGTTTCAGGTATTAAATCCCCAACTGTCTCCACCTTCATGACTACCTGGGAAATTGCAGAGTTG
CTCAACACCCTCCAGACCTGCTCTTGTTAAATGTCACTATAAAGGGGCAGAAGACGACA

hide sequence

RefSeq Acc Id:

XM_039081094 ⟹ XP_038937022

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	59,731,936 - 59,765,239 (-)	NCBI

RefSeq Acc Id:

XM_039081095 ⟹ XP_038937023

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	59,731,936 - 59,765,389 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001100296	(Get FASTA)	NCBI Sequence Viewer
	XP_008764448	(Get FASTA)	NCBI Sequence Viewer
	XP_038937022	(Get FASTA)	NCBI Sequence Viewer
	XP_038937023	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL95694	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001100296 ⟸ NM_001106826

- UniProtKB:

D4A8B1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAEEKLGMKTQVPASIESQKPRPKKAPEFPIVEKLNWLIHLYYIRKDYEACKAVIKEQLQETQG
LCEYAIYVQALIFRLEGNIQESLELFQTCAVLSPQCADNLKQVARSLFLLGKHKAATEVYNEAA
KLNQKDWEICHNLGVCYTYLKQFSKAQDQLHSALQLNKHDLTYIMLGKIHLLQGDLDKAIEIYK
KAVEFSPENTELLTTLGLLYLQLGVYQKAFEHLGNALTYDPANYKAILAAGSMMQTHGDFDVAL
TKYRVVACAIPESPPLWNNIGMCFFGKKKYVAAISCLKRANYLAPFDWKILYNLGLVHLTMQQY
ASAFHFLSAAINFQPKMGELYMLLAVALTNLEDIENAKRAYVEAVRLDKCNPLVNLNYAVLLYN
QGEKKGALAQYQEMEKKVHFLKDNNPLEFDSEMVEMAQKLGAALQVGEALVWTKPVKDPKSKHR
TNSGSKSATLQQPLGSFQALGQAMSSAAAHRKIPSGAVGAQLTKPPSLPLEPEPEPTVEASPTE
ASEQNKEK

hide sequence

RefSeq Acc Id:

XP_008764448 ⟸ XM_008766226

- Peptide Label:

isoform X3

- Sequence:

show sequence

MLGKIHLLQGDLDKAIEIYKKAVEFSPENTELLTTLGLLYLQLGVYQKAFEHLGNALTYDPANY
KAILAAGSMMQTHGDFDVALTKYRVVACAIPESPPLWNNIGMCFFGKKKYVAAISCLKRANYLA
PFDWKILYNLGLVHLTMQQYASAFHFLSAAINFQPKMGELYMLLAVALTNLEDIENAKRAYVEA
VRLDKCNPLVNLNYAVLLYNQGEKKGALAQYQEMEKKVHFLKDNNPLEFDSEMVEMAQKLGAAL
QVGEALVWTKPVKDPKSKHRTNSGSKSATLQQPLGSFQALGQAMSSAAAHRKIPSGAVGAQLTK
PPSLPLEPEPEPTVEASPTEASEQNKEK

hide sequence

RefSeq Acc Id:

ENSRNOP00000030021 ⟸ ENSRNOT00000031262

RefSeq Acc Id:	XP_038937023 ⟸ XM_039081095
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038937022 ⟸ XM_039081094
- Peptide Label:	isoform X1

RefSeq Acc Id:

ENSRNOP00000092159 ⟸ ENSRNOT00000104326

RefSeq Acc Id:

ENSRNOP00000078115 ⟸ ENSRNOT00000110213

RefSeq Acc Id:

ENSRNOP00000087657 ⟸ ENSRNOT00000119362

Protein Domains

TPR_REGION

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13696038

Promoter ID:

EPDNEW_R6562

Type:

multiple initiation site

Name:

Bbs4_1

Description:

Bardet-Biedl syndrome 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	8	64,154,380 - 64,154,440	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BUF/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1309134	AgrOrtholog
Ensembl Genes	ENSRNOG00000026171	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000030021	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000031262	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.10	UniProtKB/TrEMBL
InterPro	BBS4	UniProtKB/TrEMBL
	TPR-like_helical	UniProtKB/TrEMBL
	TPR_repeat	UniProtKB/TrEMBL
KEGG Report	rno:300754	UniProtKB/TrEMBL
NCBI Gene	300754	ENTREZGENE
PANTHER	PTHR44186	UniProtKB/TrEMBL
Pfam	TPR_8	UniProtKB/TrEMBL
PhenoGen	Bbs4	PhenoGen
PROSITE	TPR	UniProtKB/TrEMBL
SMART	TPR	UniProtKB/TrEMBL
Superfamily-SCOP	SSF48452	UniProtKB/TrEMBL
UniProt	D4A8B1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-11-05	Bbs4	Bardet-Biedl syndrome 4	Bbs4	Bardet-Biedl syndrome 4 homolog (human)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Bbs4	Bardet-Biedl syndrome 4 homolog (human)	Bbs4_predicted	Bardet-Biedl syndrome 4 homolog (human) (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Bbs4_predicted	Bardet-Biedl syndrome 4 homolog (human) (predicted)		Bardet-Biedl syndrome 4 (predicted)	Name updated	1299863	APPROVED
2005-01-12	Bbs4_predicted	Bardet-Biedl syndrome 4 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

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