Itm2b (integral membrane protein 2B)

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Gene: Itm2b (integral membrane protein 2B) Rattus norvegicus

Analyze

Symbol:

Itm2b

Name:

integral membrane protein 2B

RGD ID:

620727

Description:

Predicted to have ATP binding activity and amyloid-beta binding activity. Predicted to be involved in extrinsic apoptotic signaling pathway in absence of ligand and negative regulation of amyloid precursor protein biosynthetic process. Predicted to localize to several cellular components, including Golgi apparatus; Golgi-associated vesicle membrane; and integral component of organelle membrane. Human ortholog(s) of this gene implicated in ITM2B-related cerebral amyloid angiopathy 1 and ITM2B-related cerebral amyloid angiopathy 2. Orthologous to human ITM2B (integral membrane protein 2B); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Bri; imBRI2; immature BRI2; MGC94644; transmembrane protein BRI

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):	ITM2B (integral membrane protein 2B)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Itm2b (integral membrane protein 2B)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Itm2b (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ITM2B (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ITM2B (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Itm2b (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ITM2B (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	ITM2B (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Itm2b (integral membrane protein 2B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	ITM2B (integral membrane protein 2B)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Itm2b (integral membrane protein 2B)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	itm2bb (integral membrane protein 2Bb)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	itm2ba (integral membrane protein 2Ba)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	C25F6.7	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG3662	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|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
mRatBN7.2	15	48,545,998 - 48,568,904 (-)	NCBI
Rnor_6.0 Ensembl	15	55,254,706 - 55,277,713 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	15	55,254,703 - 55,277,713 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	15	58,977,916 - 59,000,926 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	54,005,134 - 54,028,036 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	15	54,020,916 - 54,021,022 (-)	NCBI
Celera	15	48,194,879 - 48,217,785 (-)	NCBI		Celera
Cytogenetic Map	15	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

cerebral amyloid angiopathy (ISS)

chromosome 13q14 deletion syndrome (ISO)

hypertension (ISO)

intellectual disability (ISO)

RETINAL DYSTROPHY WITH INNER RETINAL DYSFUNCTION AND GANGLION CELL ABNORMALITIES (ISO)

retinoblastoma (ISO)

vascular dementia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

1,2-dimethylhydrazine (ISO)

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

17alpha-ethynylestradiol (EXP,ISO)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

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

aflatoxin B1 (ISO)

all-trans-retinoic acid (EXP,ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

caffeine (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

chloropicrin (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

Deoxycorticosterone acetate (EXP)

diarsenic trioxide (ISO)

dieldrin (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

ethanol (ISO)

fipronil (EXP)

flutamide (EXP)

hydrogen peroxide (ISO)

isoflavones (ISO)

mercury dibromide (ISO)

nickel dichloride (EXP)

nicotine (ISO)

paclitaxel (ISO)

paracetamol (ISO)

perfluorooctanoic acid (ISO)

phenylmercury acetate (ISO)

potassium chloride (EXP)

pyrogallol (ISO)

sarin (ISO)

SB 431542 (ISO)

sunitinib (ISO)

tamoxifen (EXP,ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (EXP)

theophylline (ISO)

titanium dioxide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

extrinsic apoptotic signaling pathway in absence of ligand (ISO)

negative regulation of amyloid precursor protein biosynthetic process (IBA,ISO,ISS)

Cellular Component

endosome membrane (IEA)

extracellular space (ISO,ISS)

Golgi apparatus (IBA,ISO)

Golgi membrane (IEA)

Golgi-associated vesicle membrane (ISO,ISS)

integral component of organelle membrane (ISO,ISS)

intracellular membrane-bounded organelle (ISO)

plasma membrane (IBA,ISO,ISS)

Molecular Function

amyloid-beta binding (IBA,ISO)

ATP binding (ISO)

protein binding (IPI,ISO)

References

References - curated


1.	Fleischer A, etal., Oncogene 2002 May 9;21(20):3181-9.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Holton JL, etal., Am J Pathol 2001 Feb;158(2):515-26.
4.	Martins F, etal., Sci Rep. 2018 Feb 23;8(1):3548. doi: 10.1038/s41598-018-21453-3.
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
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

Additional References at PubMed

PMID:10526337	PMID:10679242	PMID:12477932	PMID:15489334	PMID:16027166	PMID:17965014	PMID:18097506	PMID:18524908	PMID:19056867	PMID:19114711	PMID:19199708	PMID:19849849
PMID:19946888	PMID:22194595	PMID:22871113	PMID:23376485	PMID:23533145	PMID:26515131	PMID:28176357

Genomics

Comparative Map Data

Itm2b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	15	48,545,998 - 48,568,904 (-)	NCBI
Rnor_6.0 Ensembl	15	55,254,706 - 55,277,713 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	15	55,254,703 - 55,277,713 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	15	58,977,916 - 59,000,926 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	54,005,134 - 54,028,036 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	15	54,020,916 - 54,021,022 (-)	NCBI
Celera	15	48,194,879 - 48,217,785 (-)	NCBI		Celera
Cytogenetic Map	15	q11	NCBI

ITM2B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	13	48,232,612 - 48,270,357 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	13	48,233,206 - 48,270,357 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	13	48,807,342 - 48,844,493 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	47,705,309 - 47,734,228 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	13	47,705,306 - 47,734,226	NCBI
Celera	13	29,861,986 - 29,890,942 (+)	NCBI
Cytogenetic Map	13	q14.2	NCBI
HuRef	13	29,599,469 - 29,628,426 (+)	NCBI		HuRef
CHM1_1	13	48,774,975 - 48,803,938 (+)	NCBI		CHM1_1

Itm2b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	73,599,666 - 73,622,729 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	14	73,599,666 - 73,622,729 (-)	Ensembl
GRCm38	14	73,362,226 - 73,385,289 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	73,362,226 - 73,385,289 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	73,762,038 - 73,785,078 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	14	72,096,386 - 72,119,426 (-)	NCBI			mm8
Celera	14	70,882,475 - 70,905,515 (-)	NCBI		Celera
Cytogenetic Map	14	D3	NCBI
cM Map	14	38.88	NCBI

Itm2b
(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_004955431	1,928,706 - 1,937,238 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955431	1,928,706 - 1,935,010 (+)	NCBI	ChiLan1.0	ChiLan1.0

ITM2B
(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	13	48,105,762 - 48,113,838 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	13	29,383,318 - 29,412,018 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

ITM2B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	22	3,255,139 - 3,261,440 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	22	3,255,631 - 3,261,433 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	22	3,283,458 - 3,311,398 (-)	NCBI
ROS_Cfam_1.0	22	3,368,494 - 3,396,449 (-)	NCBI
UMICH_Zoey_3.1	22	3,154,017 - 3,181,970 (-)	NCBI
UNSW_CanFamBas_1.0	22	3,216,709 - 3,244,525 (-)	NCBI
UU_Cfam_GSD_1.0	22	3,222,094 - 3,250,064 (-)	NCBI

Itm2b
(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_024404945	158,051,536 - 158,073,617 (+)	NCBI
SpeTri2.0	NW_004936565	1,535,570 - 1,557,667 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ITM2B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	19,349,133 - 19,377,917 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	19,349,088 - 19,377,931 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	19,802,615 - 19,874,829 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ITM2B
(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	3	26,149,429 - 26,178,172 (+)	NCBI
ChlSab1.1 Ensembl	3	26,149,379 - 26,177,622 (+)	Ensembl
Vero_WHO_p1.0	NW_023666057	17,730,923 - 17,759,981 (-)	NCBI

Itm2b
(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_004624748	6,598,986 - 6,622,679 (-)	NCBI

Position Markers

RH142637

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	48,564,033 - 48,564,155 (+)	MAPPER
Rnor_6.0	15	55,272,842 - 55,272,963	NCBI	Rnor6.0
Rnor_5.0	15	58,996,055 - 58,996,176	UniSTS	Rnor5.0
RGSC_v3.4	15	54,023,166 - 54,023,287	UniSTS	RGSC3.4
Celera	15	48,212,915 - 48,213,036	UniSTS
Cytogenetic Map	15	p11	UniSTS

RH129302

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	48,546,649 - 48,546,829 (+)	MAPPER
Rnor_6.0	15	55,255,355 - 55,255,534	NCBI	Rnor6.0
Rnor_5.0	15	58,978,568 - 58,978,747	UniSTS	Rnor5.0
RGSC_v3.4	15	54,005,786 - 54,005,965	UniSTS	RGSC3.4
Celera	15	48,195,531 - 48,195,710	UniSTS
Cytogenetic Map	15	p11	UniSTS

RH142259

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	48,546,673 - 48,546,831 (+)	MAPPER
Rnor_6.0	15	55,255,379 - 55,255,536	NCBI	Rnor6.0
Rnor_5.0	15	58,978,592 - 58,978,749	UniSTS	Rnor5.0
RGSC_v3.4	15	54,005,810 - 54,005,967	UniSTS	RGSC3.4
Celera	15	48,195,555 - 48,195,712	UniSTS
Cytogenetic Map	15	p11	UniSTS

RH141160

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	48,546,414 - 48,546,597 (+)	MAPPER
Rnor_6.0	15	55,255,120 - 55,255,302	NCBI	Rnor6.0
Rnor_5.0	15	58,978,333 - 58,978,515	UniSTS	Rnor5.0
RGSC_v3.4	15	54,005,551 - 54,005,733	UniSTS	RGSC3.4
Celera	15	48,195,296 - 48,195,478	UniSTS
Cytogenetic Map	15	p11	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
2298549	Neuinf12	Neuroinflammation QTL 12	3.5		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	15	1	62301382	Rat
1582251	Gluco24	Glucose level QTL 24	3.2	0.0008	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	15	10719191	55719191	Rat
2317750	Glom26	Glomerulus QTL 26	4.3		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	15	15492360	72568189	Rat
9590272	Scort14	Serum corticosterone level QTL 14	2.78	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	15	16980907	61980907	Rat
8694427	Bw163	Body weight QTL 163	4.82	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	15	16980907	61980907	Rat
2300167	Bmd63	Bone mineral density QTL 63	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	15	17249641	62249641	Rat
2300173	Bmd62	Bone mineral density QTL 62	12.8	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	15	17249641	62249641	Rat
2293688	Bss29	Bone structure and strength QTL 29	5.31	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	15	17249641	62249641	Rat
1331729	Rf42	Renal function QTL 42	3.071		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	15	18093208	81255430	Rat
61424	Scl1	Serum cholesterol level QTL 1	7.7	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	15	18513913	88036354	Rat
1578646	Bmd18	Bone mineral density QTL 18	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	15	26381041	106550657	Rat
1578647	Bmd17	Bone mineral density QTL 17	4		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	15	26381041	106550657	Rat
1578660	Bss19	Bone structure and strength QTL 19	4.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	15	26381041	106550657	Rat
10054130	Srcrt8	Stress Responsive Cort QTL 8	2.18	0.0085	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	15	28709741	73709741	Rat
1582214	Stl21	Serum triglyceride level QTL 21	3.1	0.022	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	15	33219101	89640841	Rat
1582227	Gluco30	Glucose level QTL 30	3.6	0.0003	blood glucose amount (VT:0000188)	absolute change in blood glucose level area under curve (CMO:0002034)	15	33219101	89640841	Rat
1582228	Epfw3	Epididymal fat weight QTL 3	4.1	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	33219101	89640841	Rat
1582242	Gluco28	Glucose level QTL 28	3.3	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	15	33219101	89640841	Rat
1582244	Bw79	Body weight QTL 79	4	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	33219101	89640841	Rat
631273	Lecl2	Lens clarity QTL 2		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	15	39480797	62596410	Rat
2293686	Bmd36	Bone mineral density QTL 36	7.4	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	15	39749557	79033707	Rat
2293691	Bmd37	Bone mineral density QTL 37	6.6	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	15	39749557	79033707	Rat
1598828	Glom14	Glomerulus QTL 14	2.5		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	15	41068094	86068094	Rat
7411725	Strs7	Sensitivity to stroke QTL 7	3.8		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	15	42757241	56027084	Rat
1300144	Rf23	Renal function QTL 23	3.61		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	15	43097470	106550657	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	122
Count of miRNA genes:	91
Interacting mature miRNAs:	107
Transcripts:	ENSRNOT00000023037
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									4	13	3	2
Medium	3	43	57	41	19	41	8	11	70	22	38	9	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001006963	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017599637	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF034245	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC083735	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473951	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ210227	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ210419	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212539	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212626	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212795	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212925	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213415	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218718	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219378	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219414	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219676	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229426	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230065	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000272	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000023037 ⟹ ENSRNOP00000023037

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	15	55,254,706 - 55,277,713 (-)	Ensembl

RefSeq Acc Id:

NM_001006963 ⟹ NP_001006964

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	48,545,998 - 48,568,904 (-)	NCBI
Rnor_6.0	15	55,254,703 - 55,277,713 (-)	NCBI
Rnor_5.0	15	58,977,916 - 59,000,926 (-)	NCBI
RGSC_v3.4	15	54,005,134 - 54,028,036 (-)	RGD
Celera	15	48,194,879 - 48,217,785 (-)	RGD

Sequence:

show sequence

CACTGAGCCGCTGCTGCTGTCGCGCAGTTCGCTCCTCCGCTGCAGAGTCGTGCCCTGAGCTCGG
CCGACGAGGCTGCACCCGCAGCCGGGATCCTGCCACCCGCGACCCCAGCCTTCGCCGCCGCCGC
CGCCGCCGCCGCCTAGGGCGCCCCAGGCCGCACCATGGTGAAGGTGACGTTCAACTCGGCGCTG
GCCCAAAAGGAGGCCAAGAAGGACGAGCCCAAGAGCAGCGAGGAGGCGCTCATCGCCCCTCCGG
ATGCCGTGGCGGTGGATTGCAAGGACCCGGATGACGTGGTCCCAGTTGGCCAGAGGAGAGCGTG
GTGTTGGTGCATGTGCTTTGGACTGGCCTTCATGCTCGCTGGCGTCATCCTGGGAGGAGCATAC
CTCTACAAGTATTTTGCACTTCAGCCAGATGATGTGTACTACTGTGGACTAAAGTACATCAAAG
ATGACGTCATCTTGAGTGAGCCTTCTGCAGATGCCCCAGCTGCTCGATACCAGACAATTGAAGA
GAATATTAAGATCTTTGAGGAAGACGCAGTTGAATTCATCAGTGTGCCTGTACCAGAGTTTGCG
GACAGCGATCCTGCCAACATTGTGCATGACTTTAACAAGAAACTCACTGCTTATTTGGACCTTA
ATCTGGACAAGTGCTACGTGATTCCTCTGAACACCTCCATTGTTATGCCACCCAGAAACCTGTT
GGAGCTTCTTATTAACATCAAGGCCGGGACCTACTTGCCTCAGTCATACCTCATCCATGAGCAC
ATGGTGATCACCGACCGCATCGAAAACGTGGACCACCTGGGCTTCTTCATTTACCGACTGTGTC
ACGACAAGGAAACCTACAAACTGCAGCGCAGGGAAACCATTAGAGGTATTCAGAAGCGTGAAGC
CAGTAACTGTTTCACCATTCGGCATTTTGAGAACAAATTTGCTGTGGAAACTTTAATTTGTTCT
TGAGACGTCAAGAAAAAAAGTGAGGAGAAATTCAATGCCACAGCATACCCTGCCCCTTTGTATT
TTGTGCAGTGATTGTTTTTAAAATCTTTTCATGTAAGTAGCAAACAGGGCTTCACTGTCTCTTC
ATCTCAATAATTCAATTAAAAACCATTATCTTAAAAAAAAGAAAACAAAACCTTCCTTTTTTCT
AAGTGTGGTGTCTTTGGCATTTGAGTTAGCAGATGTATGGGTTCCTAGATAAGATTTGCTTTTC
CATAGAGTTTACATACTAGGAAGAATATAACTGTCTTGACATCACTAATCTGGATTTTTGTGTT
ACTTCTGCACTTCCATGAGGGAAGGGTACCTAAAGAATAGACCTTTGCATCGCTAAGAGGACCG
CGGTGACTTGCCTGTAGATGCCGATAGCCCTGCTGCCTAGCCTGTTAGCATTTGCGGTCACCTT
CTCATTGTTGTGTTAACTACTTTAGAGGATTTCAGCCTTGATGTTTTAATATCCTAGGCCTCTG
CTGTAATAAGATTTTAGACAACTGTTTGGAATTTAAGAAACAACTCATGTTACTAATTTGTACA
GCCCATATCTGTGCAATGGAATATAAATATCACAAAGCCATGTGATGAGACTGTGCGTCGTTTT
TCCCATGAGATAAAAACCAAAGAAATGATTTGGTTCTCCATATTTTAAGGTAATCCACGTGCAT
AAAGAATGAAACTATTTTATAAAGTCTAGTTCTCTACATGCAGTTATAAAAATCAGCTTTTTAA
AAAAATAAAACAAGCCATTAATTACTAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_017599637 ⟹ XP_017455126

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	15	55,254,703 - 55,268,728 (-)	NCBI

Sequence:

show sequence

AATGGTGTAGCCAGGCTTGCCCTCCATTCACACTGCTCTTCCTGTCTCCGCTTCCTGAGCACTG
GGAGTGCAGGTGTGCACATTGCCAGCCAATCCTTCCATCCCATCGGTGTCAGATTCCACCTCAG
CGGCAGCTCCTGGGTGCCGTGCCTCGGCTCCTGCTCTGCTGCTATTCTGGAATCTAGTTCTTCC
TGCACTGTCTTCTTGCTCCATTTTGTTCTCTGTCTGCAGAAGTTTGGGGCTTTTCTCCCCATGC
TGTGAGGTCCTCCCCTCTGTGAGACTTTGTTGACAGACTCTGCTGTCCATGGTGTCTGTTCCAT
GGGGTCACAGCTTCATTTGCTTTGCCTTCACCGTTCCCTCATGGAGTTTTCAGAAGATAAACAT
TAGCTGAAAATCAATATTTGGACTTTCAGCTCCACCTTCACTGTAGCTTTTGAAAGTTTAATTA
GAATATTCCCTTTGCACTAACAATAGGCCTAATGATAATTAATAATGGATAATAATGGAAACTG
TCTGGATTATTGGCACTAATTTAAGACCTGACAAGATGACCTAGAAAAATGCACCACCATCCTC
TAATCTCCTCTCCAAAGAGCCAAGACCGCCATCGTCTGAGTGTCTGCTGGACACTGCTCACTAC
CAGTTTGGGATTTTGCTTTGGGCCTTTGTGCTCTGAGGACCCGGATGACGTGGTCCCAGTTGGC
CAGAGGAGAGCGTGGTGTTGGTGCATGTGCTTTGGACTGGCCTTCATGCTCGCTGGCGTCATCC
TGGGAGGAGCATACCTCTACAAGTATTTTGCACTTCAGCCAGATGATGTGTACTACTGTGGACT
AAAGTACATCAAAGATGACGTCATCTTGAGTGAGCCTTCTGCAGATGCCCCAGCTGCTCGATAC
CAGACAATTGAAGAGAATATTAAGATCTTTGAGGAAGACGCAGTTGAATTCATCAGTGTGCCTG
TACCAGAGTTTGCGGACAGCGATCCTGCCAACATTGTGCATGACTTTAACAAGAAACTCACTGC
TTATTTGGACCTTAATCTGGACAAGTGCTACGTGATTCCTCTGAACACCTCCATTGTTATGCCA
CCCAGAAACCTGTTGGAGCTTCTTATTAACATCAAGGCCGGGACCTACTTGCCTCAGTCATACC
TCATCCATGAGCACATGGTGATCACCGACCGCATCGAAAACGTGGACCACCTGGGCTTCTTCAT
TTACCGACTGTGTCACGACAAGGAAACCTACAAACTGCAGCGCAGGGAAACCATTAGAGGTATT
CAGAAGCGTGAAGCCAGTAACTGTTTCACCATTCGGCATTTTGAGAACAAATTTGCTGTGGAAA
CTTTAATTTGTTCTTGAGACGTCAAGAAAAAAAGTGAGGAGAAATTCAATGCCACAGCATACCC
TGCCCCTTTGTATTTTGTGCAGTGATTGTTTTTAAAATCTTTTCATGTAAGTAGCAAACAGGGC
TTCACTGTCTCTTCATCTCAATAATTCAATTAAAAACCATTATCTTAAAAAAAAGAAAACAAAA
CCTTCCTTTTTTCTAAGTGTGGTGTCTTTGGCATTTGAGTTAGCAGATGTATGGGTTCCTAGAT
AAGATTTGCTTTTCCATAGAGTTTACATACTAGGAAGAATATAACTGTCTTGACATCACTAATC
TGGATTTTTGTGTTACTTCTGCACTTCCATGAGGGAAGGGTACCTAAAGAATAGACCTTTGCAT
CGCTAAGAGGACCGCGGTGACTTGCCTGTAGATGCCGATAGCCCTGCTGCCTAGCCTGTTAGCA
TTTGCGGTCACCTTCTCATTGTTGTGTTAACTACTTTAGAGGATTTCAGCCTTGATGTTTTAAT
ATCCTAGGCCTCTGCTGTAATAAGATTTTAGACAACTGTTTGGAATTTAAGAAACAACTCATGT
TACTAATTTGTACAGCCCATATCTGTGCAATGGAATATAAATATCACAAAGCCATGTGATGAGA
CTGTGCGTCGTTTTTCCCATGAGATAAAAACCAAAGAAATGATTTGGTTCTCCATATTTTAAGG
TAATCCACGTGCATAAAGAATGAAACTATTTTATAAAGTCTAGTTCTCTACATGCAGTTATAAA
AATCAGCTTTTTAAAAAAATAAAACAAGCCATTAATTACTAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001006964	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH83735	(Get FASTA)	NCBI Sequence Viewer
	EDM02268	(Get FASTA)	NCBI Sequence Viewer
	Q5XIE8	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001006964 ⟸ NM_001006963

- UniProtKB:

Q5XIE8 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MVKVTFNSALAQKEAKKDEPKSSEEALIAPPDAVAVDCKDPDDVVPVGQRRAWCWCMCFGLAFM
LAGVILGGAYLYKYFALQPDDVYYCGLKYIKDDVILSEPSADAPAARYQTIEENIKIFEEDAVE
FISVPVPEFADSDPANIVHDFNKKLTAYLDLNLDKCYVIPLNTSIVMPPRNLLELLINIKAGTY
LPQSYLIHEHMVITDRIENVDHLGFFIYRLCHDKETYKLQRRETIRGIQKREASNCFTIRHFEN
KFAVETLICS

hide sequence

RefSeq Acc Id:

XP_017455126 ⟸ XM_017599637

- Peptide Label:

isoform X1

- Sequence:

show sequence

MHHHPLISSPKSQDRHRLSVCWTLLTTSLGFCFGPLCSEDPDDVVPVGQRRAWCWCMCFGLAFM
LAGVILGGAYLYKYFALQPDDVYYCGLKYIKDDVILSEPSADAPAARYQTIEENIKIFEEDAVE
FISVPVPEFADSDPANIVHDFNKKLTAYLDLNLDKCYVIPLNTSIVMPPRNLLELLINIKAGTY
LPQSYLIHEHMVITDRIENVDHLGFFIYRLCHDKETYKLQRRETIRGIQKREASNCFTIRHFEN
KFAVETLICS

hide sequence

RefSeq Acc Id:

ENSRNOP00000023037 ⟸ ENSRNOT00000023037

Protein Domains

BRICHOS

Transcriptome

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

Promoters

RGD ID:

13699823

Promoter ID:

EPDNEW_R10347

Type:

initiation region

Name:

Itm2b_1

Description:

integral membrane protein 2B

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	15	55,277,709 - 55,277,769	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

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 (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/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 (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)

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

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

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/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

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 (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

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

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

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

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

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 (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

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

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 (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 (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

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 (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 (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 (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:620727	AgrOrtholog
Ensembl Genes	ENSRNOG00000016271	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000023037	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000023037	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7191589	IMAGE-MGC_LOAD
InterPro	BRICHOS_dom	UniProtKB/Swiss-Prot
	ITM2	UniProtKB/Swiss-Prot
KEGG Report	rno:290364	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:94644	IMAGE-MGC_LOAD
NCBI Gene	290364	ENTREZGENE
PANTHER	PTHR10962	UniProtKB/Swiss-Prot
Pfam	BRICHOS	UniProtKB/Swiss-Prot
PhenoGen	Itm2b	PhenoGen
PROSITE	BRICHOS	UniProtKB/Swiss-Prot
SMART	BRICHOS	UniProtKB/Swiss-Prot
UniProt	ITM2B_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Itm2b	integral membrane protein 2B			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Itm2b	integral membrane protein 2B			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)

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Imported Disease Annotations - ClinVar

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