Hs1bp3 (HCLS1 binding protein 3) - Rat Genome Database

Name: Hs1bp3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| FTP Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Hs1bp3 (HCLS1 binding protein 3) Rattus norvegicus

Analyze

Symbol:

Hs1bp3

Name:

HCLS1 binding protein 3

RGD ID:

1311331

Description:

Predicted to have phosphatidylinositol binding activity. Predicted to be involved in regulation of apoptotic process. Predicted to localize to endoplasmic reticulum and mitochondrion. Human ortholog(s) of this gene implicated in essential tremor 2. Orthologous to human HS1BP3 (HCLS1 binding protein 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

HCLS1-binding protein 3; LOC313950; RGD1311331; similar to HS1 binding protein 3

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

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):	HS1BP3 (HCLS1 binding protein 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Hs1bp3 (HCLS1 binding protein 3)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Hs1bp3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HS1BP3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HS1BP3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hs1bp3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HS1BP3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	HS1BP3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hs1bp3 (HCLS1 binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Hs1bp3 (HCLS1 binding protein 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	HS1BP3 (HCLS1 binding protein 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	hs1bp3 (HCLS1 binding protein 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	6	33,517,711 - 33,548,015 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	33,517,769 - 33,548,034 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	43,302,675 - 43,333,022 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	31,872,303 - 31,902,812 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	31,872,249 - 31,904,371 (+)	NCBI
Celera	6	30,642,682 - 30,672,986 (+)	NCBI		Celera
Cytogenetic Map	6	q14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

essential tremor 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(R)-lipoic acid (ISO)

17beta-estradiol (ISO)

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

2-methylcholine (ISO)

3-chloropropane-1,2-diol (EXP)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

entinostat (ISO)

folic acid (ISO)

lipoic acid (ISO)

mercury atom (ISO)

mercury(0) (ISO)

methotrexate (ISO)

potassium dichromate (ISO)

quercetin (ISO)

resveratrol (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

Soman (EXP)

sunitinib (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

regulation of apoptotic process (ISO)

Cellular Component

endoplasmic reticulum (ISO)

mitochondrion (ISO)

Molecular Function

phosphatidylinositol binding (IEA)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	MGD data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:21699750

Genomics

Comparative Map Data

Hs1bp3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	6	33,517,711 - 33,548,015 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	33,517,769 - 33,548,034 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	43,302,675 - 43,333,022 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	31,872,303 - 31,902,812 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	31,872,249 - 31,904,371 (+)	NCBI
Celera	6	30,642,682 - 30,672,986 (+)	NCBI		Celera
Cytogenetic Map	6	q14	NCBI

HS1BP3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	20,560,448 - 20,651,130 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	20,552,934 - 20,651,661 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	20,817,564 - 20,850,867 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	20,681,045 - 20,714,345 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	2	20,679,957 - 20,713,243 (-)	NCBI
Cytogenetic Map	2	p24.1	NCBI
HuRef	2	20,574,500 - 20,607,784 (-)	NCBI		HuRef
CHM1_1	2	20,746,925 - 20,780,237 (-)	NCBI		CHM1_1

Hs1bp3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	8,363,389 - 8,393,824 (+)	NCBI	GRCm39		mm39
GRCm38	12	8,313,433 - 8,343,824 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	8,313,432 - 8,343,824 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	8,320,239 - 8,350,630 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	12	8,339,469 - 8,368,770 (+)	NCBI			mm8
Celera	12	8,707,258 - 8,737,866 (+)	NCBI		Celera
Cytogenetic Map	12	A1.1	NCBI

Hs1bp3
(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_004955469	3,106,753 - 3,133,926 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955469	3,105,897 - 3,133,918 (-)	NCBI	ChiLan1.0	ChiLan1.0

HS1BP3
(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	2A	20,718,953 - 20,752,038 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	20,720,152 - 20,752,044 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2A	20,464,789 - 20,636,827 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

HS1BP3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	17	15,579,371 - 15,623,689 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	17	15,577,552 - 15,610,141 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Hs1bp3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936493	10,830,956 - 10,859,315 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HS1BP3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	117,609,033 - 117,648,383 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	117,608,987 - 117,647,361 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	125,569,581 - 125,607,917 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HS1BP3
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1 Ensembl	14	87,043,196 - 87,077,623 (+)	Ensembl
ChlSab1.1	14	87,043,153 - 87,077,627 (+)	NCBI

Hs1bp3
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624738	3,250,066 - 3,273,273 (-)	NCBI

Position Markers

RH141619

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	33,547,808 - 33,547,989	NCBI	Rnor6.0
Rnor_5.0	6	43,332,808 - 43,332,989	UniSTS	Rnor5.0
RGSC_v3.4	6	31,902,324 - 31,902,505	UniSTS	RGSC3.4
Celera	6	30,672,779 - 30,672,960	UniSTS
Cytogenetic Map	6	q14	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
738023	Alc17	Alcohol consumption QTL 17	3.1	0.003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	6	1	35623029	Rat
1354616	Despr12	Despair related QTL 12		0.0012	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	6	1	35623029	Rat
1549905	Stresp10	Stress response QTL 10	6.83	0.0066	stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	6	1	35623029	Rat
2300176	Bmd51	Bone mineral density QTL 51	11.7	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	6	1	35623029	Rat
2300190	Bmd52	Bone mineral density QTL 52	11.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	6	1	35623029	Rat
1331743	Uae28	Urinary albumin excretion QTL 28	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	1	41917988	Rat
9589048	Scfw3	Subcutaneous fat weight QTL 3	4.57	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	6	1	42388212	Rat
9589129	Insul24	Insulin level QTL 24	19.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	6	1	42388212	Rat
7411603	Foco13	Food consumption QTL 13	5.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	42388212	Rat
7411542	Bw127	Body weight QTL 127	5.5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	1	42388212	Rat
8552962	Pigfal16	Plasma insulin-like growth factor 1 level QTL 16	9.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	1	42388212	Rat
2293709	Bss23	Bone structure and strength QTL 23	5.18	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	6	1	43665660	Rat
2293650	Bss31	Bone structure and strength QTL 31	5.05	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	6	1	43665660	Rat
2293656	Bss28	Bone structure and strength QTL 28	6.79	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	6	1	43665660	Rat
7411584	Foco4	Food consumption QTL 4	4.3	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	44015370	Rat
738024	Sach5	Saccharine consumption QTL 5	3.9	0.00039	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	6	1	44570292	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	75623393	Rat
2292589	Emca10	Estrogen-induced mammary cancer QTL 10		0.048	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	1120393	46120393	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	1120393	75023446	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	2537030	111715717	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	6161722	76002731	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	6161722	76002731	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	7009971	115379601	Rat
634322	Bw12	Body weight QTL 12	0		body mass (VT:0001259)	body weight (CMO:0000012)	7	10173862	55173862	Rat
1300128	Rf16	Renal function QTL 16	3.89		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	13122958	34367603	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	13122958	57516539	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	16810107	61810107	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	16810107	61810107	Rat
8552910	Pigfal5	Plasma insulin-like growth factor 1 level QTL 5	4.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	19417887	64417887	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	21515302	65784818	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	257
Count of miRNA genes:	171
Interacting mature miRNAs:	205
Transcripts:	ENSRNOT00000007991
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		2	2	2	2			38	35	31	11
Low		43	55	39	17	39	8	11	36		10		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_001071788	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_233975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAHX01042567	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC142360	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224595	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000007991 ⟹ ENSRNOP00000007991

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	33,517,769 - 33,548,034 (+)	Ensembl

RefSeq Acc Id:

XM_001071788 ⟹ XP_001071788

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	6	30,642,682 - 30,672,986 (+)	NCBI

Sequence:

show sequence

CGGAGCGGGGCGGGGCAGGGACGCAGCGACGCCCAGGACGCCAGATCCCGTGACCGTCCGCCAG
ACCGCAGCCGATATGCAGTCCCCGGCGGTGCTCGTCACCTCCAGGCAAGTTCAGAATGCGCACA
CGGGCCTCGACCTGACTGTACCACAGCACCAGGAGGTGCGGGGTAAGATGATGTCAGGCCATGT
GGAGTACCAGATCCTGGTGGTGACCCGGTTGGCTGTGTTCAAGTCAGCCAAGCACCGGCCCGAG
GATGTCGTCCAGTTCTTGGTCTCCAAAAAATACAGCGAGATCGAGGAGTTTTACCAGAAACTGT
ACAGTCGTTACCCAGAAGCCAGCCTGCCCCCACTGCCTAGGAAGGTCCTGTTTGTCGGGGAGTC
TGACATCCGGGAAAGGAGAGCCATGTTTGATGAGATTCTACGCTGTGTCTCCAAGGATGCCCAG
TTGGCGGGCAGCCCAGAGCTGCTAGAATTCTTAGGCACCAGGTCCCCGGGGGCTACAGGCTTTG
CCACCCGAGATCCCTCTGTCTTGGATGAGACAGCCAGCCGGCCAGGGGACAGTGATGAGGCTTT
TGACTTCTTTGAGCAACAGGATGAAGTGCAGCCACCCACATTGGGCCTGAGCAACAAGAATGTT
GAGAAGTCCTTGGAAGAAGAGGAGGAGGAGGAGGAGATACTGGATCCCCTGGGCATCATGCGCT
CCAAGAAGCCTAAGAAACACCAAGAAGTGGCCATGAGGACCAAGCCTTCACCTCGGCTCACCAT
CTTTGACGAGGAGGTAGACCCTGACGAGGGGCTCTTTAGCTCAGACAAGAAGGTGTCCCCTCGG
AGACCTCTGGGGACCACAGAGGACCCCCTGAAGCTGTTTGACGACCCTGACCTAGGTGGGGCTG
TCTCCCTGGGTGACCCTTTACTGCTGCCGGCTGCCCATGAGAGTAGAGGGCCCACATCCAGCCC
AGAACACAGGGATGCCTCCAAAGAGCTGTTCAGAGTTGAAGAGGACCTGGACCAGATTCTGAAC
CTGGGATCTGAACCAAAACCCAAGCCCCAGCTGAAGCCCAAGCCTCTAGTCCCGTCTAAGCCAG
CATTACCCAGGAAGCCAACTGTGCCCCCCGCAGTGGGCCCATCAGGAACTGGGGCTGGGCCACA
GAAGCAGCAACAGATCCAGGCTATGGATGAAATGGACATCTTGCAGTATATCCGGGACCAGGAC
ACACTTGCCCAAGACTCCCCCAGCCTCTTCTGACTTCTCCACAACCCTGCCCTTCAAACTATGC
TGGGCCTGGGGAGGAAGCCTGTGTGTCAATATGTGGGTTCTGCTTGCAAGGCAAGGACCACCAA
TGGAAGTGGAACCCTGGACCCTCCCAGTCCCCCCACATCTTTCCCTTTTCTCCTGGGCTATGGG
ATAGACAAGGACTCTGCAGAATGTAGAGCTGAGAACACCATAGAAATCAAGCCGCATCATCTCC
ACCCAGCTGGCTGTAAGAAGAAGGTTATTTGTGGGCTCGTCTTGCTCAACGGGGACCTGACCTC
AAGTGGGGAATGAGATCGGAGGACAGTGTCCCCCAGGGAAAGGACATCTTCTGCATACTTGTTC
CCACTGGCCAGCTCAGCATGGGAAGGAGTGTGAGCTTTGGCTAGGCCAAAGGGGTCCCTGGGAC
AGGCTGCTCCAGACTCTCTATTTGGCATAGCTGCTAGGGCCCCGAGGTGTGTTCTGAGGAGAAA
GGCCAGCTCCCCTGACTGCCCTGACCCAAGTCCCTTCTTAGTCTCTTCTGGCTTCCAGTGCTAA
GAAGAAACCATAGGCCCAGCCTTGCCTTTCTAGGGCACAGAGGCTCCCAGGACCCCATGCCTTC
CACTTCCTTCCCCAGAAAAGGGCCTGGCTAGCCCATGGCCTTTTGGATGCAGCTGTCAACAGAG
TAGGTCCTAGCATCTCCCAGGGTTTGGCCCATGGGGTATGAGGCTCTGAGGCCTTGTCTGCCCT
CAGGATCTGAACTTGTTCCTTAGCCTTTCTCCTGTGGAGCCACCAGCCAAGGGAGAAGGAACTG
TGCCCCAGGGCAATCCCGTGCCTTCTAGTAGATGCTGTTTTATGGAACGAAGGACCTTAGAGTA
TTTTGTGTCAGAAACATTTTATTTGTAATGAAACACATAGGGTTTTTGTTTTGTTTTGTTTTTG
TCTTTTGCTTTTTTGTTTTTTCAGAATGCAGCCATTTTGTTCCTTGGGTCAACTGGGCTTCACT
GAGGCATTAGAAGGGCCCAGTTGGGTCCAAGAGCCACTTTCAGGAATCTCCAAGTAGCACGGTT
CAATTTTTTGTTGCCGTCAGTGTCGGGGTCCCCAGCTCCTACCCTGTAGTAAGACCTATAGGAT
CAGTCTAAGAGTATCAAGTCGGACCTATCTTTCATCTCACCATGTCCCTTGTCACCTGCCTCGA
TCTGAGCAGGCCACCTGCCCAGGCTGAAAACGGTTCTAGGCGGAGGACCAGAGTACCCTGCTTT
ACTAGGTTGAGGGTCTCCCCAGAGCCTTGAACTGACTCTAGATAGCCTCGACCCCAACTCTACT
TCCCCTTCACCAGCAGGCCTTCACCCCTCCATCTCTTGGTGCCCAACACTCAGCCCAGTGTCCA
GAAGCCCTTCCTCACTGACTGCAAAGGCAGGTTCACGTGGCCTAGTCTTGTGTAGAGCTACCCT
ACTGTGTTCCCTGGGCATCTTTGGACCCTTCTCCCTCTATATCCACTCCTCTGTGCCTTGGCTA
CCAGCTCTCTACCTCTCTTTCATACACACCTTGCACCTGCTTTGGGTGTTAGATGACATAGGAG
CCATGGGTGTGTAGGGGCTTGGATGACCACAGACTGATCCCCACCTGGTGTTCCTAACCGTACC
TGACCTGACCTACCACTCTCTAAGGTGGTTTTGCCCACTAGTGGGGATGTCTACTGTGGAGATT
TTGGGATACCTTGGCGTGGGTGTTTGCCCCACAGATAGCATTTTCCCAATCATGATTTGTTTTG
ATCACAGGTCTGTGACCTACAGCCAATCTATGTCTCCCAGCTACCCAGTAAAGTCTGTGTGTGA
CAAA

hide sequence

RefSeq Acc Id:

XM_233975 ⟹ XP_233975

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	33,517,711 - 33,548,015 (+)	NCBI
Rnor_5.0	6	43,302,675 - 43,333,022 (+)	NCBI
RGSC_v3.4	6	31,872,303 - 31,902,812 (+)	RGD

Sequence:

show sequence

CGGAGCGGGGCGGGGCAGGGACGCAGCGACGCCCAGGACGCCAGATCCCGTGACCGTCCGCCAG
ACCGCAGCCGATATGCAGTCCCCGGCGGTGCTCGTCACCTCCAGGCAAGTTCAGAATGCGCACA
CGGGCCTCGACCTGACTGTACCACAGCACCAGGAGGTGCGGGGTAAGATGATGTCAGGCCATGT
GGAGTACCAGATCCTGGTGGTGACCCGGTTGGCTGTGTTCAAGTCAGCCAAGCACCGGCCCGAG
GATGTCGTCCAGTTCTTGGTCTCCAAAAAATACAGCGAGATCGAGGAGTTTTACCAGAAACTGT
ACAGTCGTTACCCAGAAGCCAGCCTGCCCCCACTGCCTAGGAAGGTCCTGTTTGTCGGGGAGTC
TGACATCCGGGAAAGGAGAGCCATGTTTGATGAGATTCTACGCTGTGTCTCCAAGGATGCCCAG
TTGGCGGGCAGCCCAGAGCTGCTAGAATTCTTAGGCACCAGGTCCCCGGGGGCTACAGGCTTTG
CCACCCGAGATCCCTCTGTCTTGGATGAGACAGCCAGCCGGCCAGGGGACAGTGATGAGGCTTT
TGACTTCTTTGAGCAACAGGATGAAGTGCAGCCACCCACATTGGGCCTGAGCAACAAGAATGTT
GAGAAGTCCTTGGAAGAAGAGGAGGAGGAGGAGGAGATACTGGATCCCCTGGGCATCATGCGCT
CCAAGAAGCCTAAGAAACACCAAGAAGTGGCCATGAGGACCAAGCCTTCACCTCGGCTCACCAT
CTTTGACGAGGAGGTAGACCCTGACGAGGGGCTCTTTAGCTCAGACAAGAAGGTGTCCCCTCGG
AGACCTCTGGGGACCACAGAGGACCCCCTGAAGCTGTTTGACGACCCTGACCTAGGTGGGGCTG
TCTCCCTGGGTGACCCTTTACTGCTGCCGGCTGCCCATGAGAGTAGAGGGCCCACATCCAGCCC
AGAACACAGGGATGCCTCCAAAGAGCTGTTCAGAGTTGAAGAGGACCTGGACCAGATTCTGAAC
CTGGGATCTGAACCAAAACCCAAGCCCCAGCTGAAGCCCAAGCCTCTAGTCCCGTCTAAGCCAG
CATTACCCAGGAAGCCAACTGTGCCCCCCGCAGTGGGCCCATCAGGAACTGGGGCTGGGCCACA
GAAGCAGCAACAGATCCAGGCTATGGATGAAATGGACATCTTGCAGTATATCCGGGACCAGGAC
ACACTTGCCCAAGACTCCCCCAGCCTCTTCTGACTTCTCCACAACCCTGCCCTTCAAACTATGC
TGGGCCTGGGGAGGAAGCCTGTGTGTCAATATGTGGGTTCTGCTTGCAAGGCAAGGACCACCAA
TGGAAGTGGAACCCTGGACCCTCCCAGTCCCCCCACATCTTTCCCTTTTCTCCTGGGCTATGGG
ATAGACAAGGACTCTGCAGAATGTAGAGCTGAGAACACCATAGAAATCAAGCCGCATCATCTCC
ACCCAGCTGGCTGTAAGAAGAAGGTTATTTGTGGGCTCGTCTTGCTCAACGGGGACCTGACCTC
AAGTGGGGAATGAGATCGGAGGACAGTGTCCCCCAGGGAAAGGACATCTTCTGCATACTTGTTC
CCACTGGCCAGCTCAGCATGGGAAGGAGTGTGAGCTTTGGCTAGGCCAAAGGGGTCCCTGGGAC
AGGCTGCTCCAGACTCTCTATTTGGCATAGCTGCTAGGGCCCCGAGGTGTGTTCTGAGGAGAAA
GGCCAGCTCCCCTGACTGCCCTGACCCAAGTCCCTTCTTAGTCTCTTCTGGCTTCCAGTGCTAA
GAAGAAACCATAGGCCCAGCCTTGCCTTTCTAGGGCACAGAGGCTCCCAGGACCCCATGCCTTC
CACTTCCTTCCCCAGAAAAGGGCCTGGCTAGCCCATGGCCTTTTGGATGCAGCTGTCAACAGAG
TAGGTCCTAGCATCTCCCAGGGTTTGGCCCATGGGGTATGAGGCTCTGAGGCCTTGTCTGCCCT
CAGGATCTGAACTTGTTCCTTAGCCTTTCTCCTGTGGAGCCACCAGCCAAGGGAGAAGGAACTG
TGCCCCAGGGCAATCCCGTGCCTTCTAGTAGATGCTGTTTTATGGAACGAAGGACCTTAGAGTA
TTTTGTGTCAGAAACATTTTATTTGTAATGAAACACATAGGGTTTTTGTTTTGTTTTGTTTTTG
TCTTTTGCTTTTTTGTTTTTTCAGAATGCAGCCATTTTGTTCCTTGGGTCAACTGGGCTTCACT
GAGGCATTAGAAGGGCCCAGTTGGGTCCAAGAGCCACTTTCAGGAATCTCCAAGTAGCACGGTT
CAATTTTTTGTTGCCGTCAGTGTCGGGGTCCCCAGCTCCTACCCTGTAGTAAGACCTATAGGAT
CAGTCTAAGAGTATCAAGTCGGACCTATCTTTCATCTCACCATGTCCCTTGTCACCTGCCTCGA
TCTGAGCAGGCCACCTGCCCAGGCTGAAAACGGTTCTAGGCGGAGGACCAGAGTACCCTGCTTT
ACTAGGTTGAGGGTCTCCCCAGAGCCTTGAACTGACTCTAGATAGCCTCGACCCCAACTCTACT
TCCCCTTCACCAGCAGGCCTTCACCCCTCCATCTCTTGGTGCCCAACACTCAGCCCAGTGTCCA
GAAGCCCTTCCTCACTGACTGCAAAGGCAGGTTCACGTGGCCTAGTCTTGTGTAGAGCTACCCT
ACTGTGTTCCCTGGGCATCTTTGGACCCTTCTCCCTCTATATCCACTCCTCTGTGCCTTGGCTA
CCAGCTCTCTACCTCTCTTTCATACACACCTTGCACCTGCTTTGGGTGTTAGATGACATAGGAG
CCATGGGTGTGTAGGGGCTTGGATGACCACAGACTGATCCCCACCTGGTGTTCCTAACCGTACC
TGACCTGACCTACCACTCTCTAAGGTGGTTTTGCCCACTAGTGGGGATGTCTACTGTGGAGATT
TTGGGATACCTTGGCGTGGGTGTTTGCCCCACAGATAGCATTTTCCCAATCATGATTTGTTTTG
ATCACAGGTCTGTGACCTACAGCCAATCTATGTCTCCCAGCTACCCAGTAAAGTCTGTGTGTGA
CAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_001071788	(Get FASTA)	NCBI Sequence Viewer
	XP_233975	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM03072	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_001071788 ⟸ XM_001071788

- UniProtKB:

D4A6D9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MQSPAVLVTSRQVQNAHTGLDLTVPQHQEVRGKMMSGHVEYQILVVTRLAVFKSAKHRPEDVVQ
FLVSKKYSEIEEFYQKLYSRYPEASLPPLPRKVLFVGESDIRERRAMFDEILRCVSKDAQLAGS
PELLEFLGTRSPGATGFATRDPSVLDETASRPGDSDEAFDFFEQQDEVQPPTLGLSNKNVEKSL
EEEEEEEEILDPLGIMRSKKPKKHQEVAMRTKPSPRLTIFDEEVDPDEGLFSSDKKVSPRRPLG
TTEDPLKLFDDPDLGGAVSLGDPLLLPAAHESRGPTSSPEHRDASKELFRVEEDLDQILNLGSE
PKPKPQLKPKPLVPSKPALPRKPTVPPAVGPSGTGAGPQKQQQIQAMDEMDILQYIRDQDTLAQ
DSPSLF

hide sequence

RefSeq Acc Id:

XP_233975 ⟸ XM_233975

- UniProtKB:

D4A6D9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MQSPAVLVTSRQVQNAHTGLDLTVPQHQEVRGKMMSGHVEYQILVVTRLAVFKSAKHRPEDVVQ
FLVSKKYSEIEEFYQKLYSRYPEASLPPLPRKVLFVGESDIRERRAMFDEILRCVSKDAQLAGS
PELLEFLGTRSPGATGFATRDPSVLDETASRPGDSDEAFDFFEQQDEVQPPTLGLSNKNVEKSL
EEEEEEEEILDPLGIMRSKKPKKHQEVAMRTKPSPRLTIFDEEVDPDEGLFSSDKKVSPRRPLG
TTEDPLKLFDDPDLGGAVSLGDPLLLPAAHESRGPTSSPEHRDASKELFRVEEDLDQILNLGSE
PKPKPQLKPKPLVPSKPALPRKPTVPPAVGPSGTGAGPQKQQQIQAMDEMDILQYIRDQDTLAQ
DSPSLF

hide sequence

RefSeq Acc Id:

ENSRNOP00000007991 ⟸ ENSRNOT00000007991

Protein Domains

Transcriptome

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

Promoters

RGD ID:

13694490

Promoter ID:

EPDNEW_R5007

Type:

multiple initiation site

Name:

Hs1bp3_1

Description:

HCLS1 binding protein 3

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	6	33,517,773 - 33,517,833	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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/SsN (MCW)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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/Ox (RGD)

Visual

CSV

TAB

Printer

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

LE/Stm (RGD)

Visual

CSV

TAB

Printer

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 (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

M520/N (MCW)

Visual

CSV

TAB

Printer

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

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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/Gcrc (RGD)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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 (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (MCW)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
6	43312737	43312738	C	T	snv	MNS/Gib (KNAW), DOB/Oda (KyushuU), SDLEF7/Barth (UDEL)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
6	33527804	33527805	C	T	snv	MNS/Gib (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
6	31882320	31882321	C	T	snv	MNS/Gib (ICL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311331	AgrOrtholog
Ensembl Genes	ENSRNOG00000006062	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000007991	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000007991	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.1520.10	UniProtKB/TrEMBL
InterPro	HS1BP3	UniProtKB/TrEMBL
	HS1BP3_PX	UniProtKB/TrEMBL
	IPR001683	UniProtKB/TrEMBL
	PX_dom_sf	UniProtKB/TrEMBL
KEGG Report	rno:313950	UniProtKB/TrEMBL
NCBI Gene	313950	ENTREZGENE
PANTHER	PTHR14431	UniProtKB/TrEMBL
Pfam	PF00787	UniProtKB/TrEMBL
PhenoGen	Hs1bp3	PhenoGen
PROSITE	PS50195	UniProtKB/TrEMBL
SMART	SM00312	UniProtKB/TrEMBL
Superfamily-SCOP	64268	UniProtKB/TrEMBL
UniGene	Rn.23111	ENTREZGENE
UniProt	D4A6D9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-27	Hs1bp3	HCLS1 binding protein 3	RGD1311331_predicted	similar to HS1 binding protein 3 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	RGD1311331_predicted	similar to HS1 binding protein 3 (predicted)	LOC313950_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC313950_predicted	similar to HS1 binding protein 3 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

Imported Disease Annotations - OMIM