Cd4 (Cd4 molecule) - Rat Genome Database

Name: Cd4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Cd4 (Cd4 molecule) Rattus norvegicus

Analyze

Symbol:

Cd4

Name:

Cd4 molecule

RGD ID:

2306

Description:

Exhibits immunoglobulin binding activity; protein tyrosine kinase binding activity; and signaling receptor binding activity. Involved in several processes, including positive regulation of calcium ion transport into cytosol; response to estradiol; and response to vitamin D. Localizes to external side of plasma membrane. Used to study septic arthritis and sialadenitis. Orthologous to human CD4 (CD4 molecule); PARTICIPATES IN Arf family mediated signaling pathway; interleukin-12 signaling pathway; interleukin-23 signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

CD4 antigen; CD4 antigen (p55); p55; T-cell surface antigen T4/Leu-3; T-cell surface glycoprotein CD4; W3/25; W3/25 antigen

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):	CD4 (CD4 molecule)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Cd4 (CD4 antigen)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Cd4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CD4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CD4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cd4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CD4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CD4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cd4 (CD4 molecule)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Cd4 (CD4 antigen)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	CD4 (CD4 molecule)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	cd4-1 (CD4-1 molecule)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|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	4	157,668,878 - 157,695,366 (-)	NCBI
Rnor_6.0 Ensembl	4	157,383,052 - 157,408,176 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	157,381,862 - 157,408,357 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	224,399,640 - 224,426,134 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	160,988,512 - 161,014,038 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	161,250,744 - 161,258,974 (-)	NCBI
Celera	4	146,407,680 - 146,432,465 (-)	NCBI		Celera
RH 3.4 Map	4	1003.4	RGD
Cytogenetic Map	4	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

antiphospholipid syndrome (ISO)

autoimmune thyroiditis (ISO)

Corneal Graft Rejection (IMP)

COVID-19 (ISO)

Duchenne muscular dystrophy (ISO)

Experimental Arthritis (IMP,ISO)

Experimental Autoimmune Encephalomyelitis (IEP,IMP)

Hyperphosphatemic Familial Tumoral Calcinosis 1 (ISO)

Nerve Degeneration (ISO)

peroxisome biogenesis disorder 2B (ISO)

septic arthritis (IMP)

severe acute respiratory syndrome (ISO)

sialadenitis (IMP)

systemic lupus erythematosus (ISO)

T-Cell OKT4 Deficiency (ISO)

Transplant Rejection (IMP,ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

(S)-nicotine (ISO)

1,2-dichloroethane (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP)

17beta-estradiol 3-benzoate (EXP)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2-naphthylamine (ISO)

5-aza-2'-deoxycytidine (ISO)

acetamide (EXP)

aflatoxin B1 (EXP,ISO)

all-trans-retinoic acid (ISO)

aluminium hydroxide (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

antirheumatic drug (ISO)

asbestos (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP)

buta-1,3-diene (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

cis-caffeic acid (ISO)

cisplatin (ISO)

clofibrate (ISO)

cocaine (ISO)

cyclophosphamide (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

dichlorine (EXP)

dichloroacetic acid (ISO)

dichloromethane (EXP)

dienogest (ISO)

diethylstilbestrol (ISO)

endosulfan (EXP)

ethylbenzene (EXP)

gentamycin (EXP)

immunological adjuvant (ISO)

methotrexate (ISO)

mifepristone (ISO)

N-ethyl-N-nitrosourea (ISO)

N-nitrosodiethylamine (EXP)

nickel atom (ISO)

nicotine (ISO)

ozone (EXP)

paracetamol (ISO)

phorbol 13-acetate 12-myristate (ISO)

Ptaquiloside (ISO)

resveratrol (ISO)

rimexolone (ISO)

rotenone (EXP)

silicon dioxide (ISO)

sodium arsenite (ISO)

sulindac sulfide (ISO)

testosterone (EXP)

tetrachloroethene (ISO)

theophylline (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

toluene 2,4-diisocyanate (ISO)

trans-caffeic acid (ISO)

trichloroethene (EXP)

triptonide (ISO)

vinclozolin (EXP)

zinc atom (EXP,ISO)

zinc(0) (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adaptive immune response (IEA)

cell adhesion (IEA)

cell surface receptor signaling pathway (ISO)

cellular response to granulocyte macrophage colony-stimulating factor stimulus (ISO)

defense response to Gram-negative bacterium (ISO)

helper T cell enhancement of adaptive immune response (ISO)

induction by virus of host cell-cell fusion (ISO)

interleukin-15-mediated signaling pathway (IBA,ISO)

macrophage differentiation (ISO)

maintenance of protein location in cell (ISO)

positive regulation of calcium ion transport into cytosol (IDA)

positive regulation of calcium-mediated signaling (ISO)

positive regulation of ERK1 and ERK2 cascade (IBA,ISO)

positive regulation of I-kappaB kinase/NF-kappaB signaling (ISO)

positive regulation of kinase activity (ISO)

positive regulation of MAPK cascade (ISO)

positive regulation of monocyte differentiation (ISO)

positive regulation of peptidyl-tyrosine phosphorylation (ISO)

positive regulation of protein kinase activity (ISO)

positive regulation of protein phosphorylation (ISO)

positive regulation of T cell activation (ISO)

positive regulation of T cell proliferation (IMP)

positive regulation of transcription, DNA-templated (ISO)

positive regulation of viral entry into host cell (ISO)

regulation of calcium ion transport (ISO)

regulation of T cell activation (ISO)

response to estradiol (IEP)

response to vitamin D (IEP)

T cell activation (IBA,IMP)

T cell differentiation (ISO,ISS)

T cell selection (ISO,ISS)

Cellular Component

cell surface (ISO)

endoplasmic reticulum lumen (ISO)

endoplasmic reticulum membrane (ISO)

external side of plasma membrane (IBA,IDA,ISO)

integral component of plasma membrane (ISO)

membrane raft (IBA,ISO)

plasma membrane (IDA,ISO)

Molecular Function

coreceptor activity (IEA)

enzyme binding (ISO)

identical protein binding (ISO)

immunoglobulin binding (IDA)

interleukin-16 binding (ISO)

interleukin-16 receptor activity (ISO)

MHC class II protein binding (IBA,ISO)

MHC class II protein complex binding (ISO,ISS)

protein binding (ISO)

protein homodimerization activity (ISO)

protein kinase binding (IPI,ISO)

protein tyrosine kinase binding (IBA,IDA,ISO)

signaling receptor binding (IPI)

zinc ion binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

antigen processing and presentation pathway (IEA)

Arf family mediated signaling pathway (ISO)

interleukin-12 signaling pathway (ISO)

interleukin-23 signaling pathway (ISO)

primary immunodeficiency pathway (IEA)

T cell receptor signaling pathway (IEA)

References

References - curated


1.	Ayliffe W, etal., Br J Ophthalmol. 1992 Oct;76(10):602-6.
2.	Bakker TR, etal., Eur J Immunol. 2002 Jul;32(7):1924-32. doi: 10.1002/1521-4141(200207)32:7<1924::AID-IMMU1924>3.0.CO;2-N.
3.	Beyers AD, etal., Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2945-9.
4.	Chong AS, etal., Xenotransplantation. 2000 Nov;7(4):275-83.
5.	Clark SJ, etal., Proc Natl Acad Sci U S A 1987 Mar;84(6):1649-53.
6.	Davis SJ, etal., J Mol Biol. 1990 May 5;213(1):7-10.
7.	Fiori P, etal., Int Immunol. 1997 Apr;9(4):541-5.
8.	Frank GD and Parnes JR, J Immunol. 1998 Jan 15;160(2):634-42.
9.	Furuya T, etal., Hum Mol Genet 2000 Sep 22;9(15):2241-50
10.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11.	GOA data from the GO Consortium
12.	Greiner DL, etal., Cell Immunol. 1991 Jul;135(2):354-9.
13.	Habasque C, etal., Mol Hum Reprod 2002 May;8(5):419-25.
14.	Jefferies WA, etal., J Exp Med. 1985 Jul 1;162(1):117-27.
15.	Kong SL, etal., Virus Res. 2009 Nov;145(2):260-9. Epub 2009 Jul 25.
16.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
17.	Li S, etal., JCI Insight. 2020 May 19. pii: 138070. doi: 10.1172/jci.insight.138070.
18.	MGD data from the GO Consortium
19.	Nabozny GH, etal., Cell Immunol. 1991 Nov;138(1):185-96.
20.	Nakatsuji T Tohoku J Exp Med. 1999 Mar;187(3):215-25.
21.	Nataf S, etal., J Neuropathol Exp Neurol. 1996 Aug;55(8):904-14.
22.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
23.	Nissler K, etal., Ann Rheum Dis. 2004 Nov;63(11):1470-7.
24.	OMIM Disease Annotation Pipeline
25.	Pipeline to import KEGG annotations from KEGG into RGD
26.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27.	Pohlers D, etal., Arthritis Res. 2002;4(3):184-9. Epub 2002 Jan 8.
28.	Rabanal M, etal., Oligonucleotides. 2003;13(4):217-28.
29.	RGD automated data pipeline
30.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31.	RGD automated import pipeline for gene-chemical interactions
32.	Sakai T, etal., J Vet Med Sci. 1996 Nov;58(11):1125-7.
33.	Sayegh MH, etal., Transplantation. 1991 Feb;51(2):296-9.
34.	Sedgwick JD and Mason DW, J Neuroimmunol. 1986 Dec;13(2):217-32.
35.	Seong RH, etal., Nature. 1992 Apr 23;356(6371):718-20.
36.	Tomer Y, etal., Arthritis Rheum. 1994 Aug;37(8):1236-44.
37.	Van den Broek MF, etal., Eur J Immunol. 1992 Jan;22(1):57-61.
38.	Yao Z, etal., Aging (Albany NY). 2020 May 2;12(9):7639-7651. doi: 10.18632/aging.103101. Epub 2020 May 2.
39.	Zheng Y, etal., J Leukoc Biol. 1989 Nov;46(5):493-6.

Additional References at PubMed

PMID:1832488	PMID:1901411	PMID:2113054	PMID:2118992	PMID:2784195	PMID:2823150	PMID:3262426	PMID:7477352	PMID:7477353	PMID:7486703	PMID:7589135	PMID:7630421
PMID:7688139	PMID:7930593	PMID:8124721	PMID:8493535	PMID:8512039	PMID:8524870	PMID:8612131	PMID:8755570	PMID:8769481	PMID:8788039	PMID:9133426	PMID:9166430
PMID:9168119	PMID:9208839	PMID:9668045	PMID:10072077	PMID:10704459	PMID:10943842	PMID:11390434	PMID:11535811	PMID:12421911	PMID:12444132	PMID:14517216	PMID:14609575
PMID:14688352	PMID:15128768	PMID:15322158	PMID:15368291	PMID:15728238	PMID:15795238	PMID:15843532	PMID:16223484	PMID:16287714	PMID:16455951	PMID:16973387	PMID:17082577
PMID:17213291	PMID:17357106	PMID:17604280	PMID:18622289	PMID:18641307	PMID:18776904	PMID:18836449	PMID:19008373	PMID:19246105	PMID:19333378	PMID:19344468	PMID:19349303
PMID:19376373	PMID:19723499	PMID:19838199	PMID:19934022	PMID:20399120	PMID:20706986	PMID:20709950	PMID:21460847	PMID:21508411	PMID:21745657	PMID:22072979	PMID:24942581
PMID:26467126	PMID:29772575

Genomics

Candidate Gene Status

	Cd4 is a candidate Gene for QTL Ciaa4
	Cd4 is a candidate Gene for QTL Cia24

Comparative Map Data

Cd4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	157,668,878 - 157,695,366 (-)	NCBI
Rnor_6.0 Ensembl	4	157,383,052 - 157,408,176 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	157,381,862 - 157,408,357 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	224,399,640 - 224,426,134 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	160,988,512 - 161,014,038 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	161,250,744 - 161,258,974 (-)	NCBI
Celera	4	146,407,680 - 146,432,465 (-)	NCBI		Celera
RH 3.4 Map	4	1003.4	RGD
Cytogenetic Map	4	q42	NCBI

CD4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	6,786,858 - 6,820,799 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	6,789,528 - 6,820,799 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	6,898,694 - 6,929,965 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	6,768,912 - 6,800,237 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	6,769,004 - 6,800,235	NCBI
Celera	12	8,515,970 - 8,547,252 (+)	NCBI
Cytogenetic Map	12	p13.31	NCBI
HuRef	12	6,751,975 - 6,783,457 (+)	NCBI		HuRef
CHM1_1	12	6,897,616 - 6,928,653 (+)	NCBI		CHM1_1

Cd4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	124,841,656 - 124,865,210 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	6	124,841,655 - 124,865,184 (-)	Ensembl
GRCm38	6	124,864,693 - 124,888,247 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	124,864,692 - 124,888,221 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	124,814,711 - 124,838,227 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	6	124,830,312 - 124,853,828 (-)	NCBI			mm8
Celera	6	126,540,818 - 126,564,333 (-)	NCBI		Celera
Cytogenetic Map	6	F2	NCBI
cM Map	6	59.17	NCBI

Cd4
(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_004955413	4,408,390 - 4,421,535 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955413	4,400,326 - 4,422,110 (+)	NCBI	ChiLan1.0	ChiLan1.0

CD4
(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	12	6,834,011 - 6,864,204 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	6,834,011 - 6,864,204 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	12	6,920,587 - 6,951,814 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CD4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	38,204,003 - 38,250,771 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	38,204,003 - 38,250,771 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	8,365,799 - 8,412,893 (+)	NCBI
ROS_Cfam_1.0	27	38,555,396 - 38,606,503 (-)	NCBI
UMICH_Zoey_3.1	27	38,430,814 - 38,477,462 (-)	NCBI
UNSW_CanFamBas_1.0	27	38,472,036 - 38,518,728 (-)	NCBI
UU_Cfam_GSD_1.0	27	7,845,022 - 7,891,631 (+)	NCBI

Cd4
(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	102,330,202 - 102,362,409 (-)	NCBI
SpeTri2.0	NW_004936709	997,776 - 1,022,791 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CD4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	63,892,132 - 63,918,669 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	63,892,129 - 63,918,547 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	66,326,568 - 66,353,856 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CD4
(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	11	6,824,797 - 6,856,440 (+)	NCBI
ChlSab1.1 Ensembl	11	6,825,245 - 6,853,852 (+)	Ensembl

Cd4
(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_004624860	3,470,886 - 3,492,247 (+)	NCBI

Position Markers

RH94477

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	4	157,383,077 - 157,383,250	NCBI	Rnor6.0
Rnor_5.0	4	224,400,855 - 224,401,028	UniSTS	Rnor5.0
RGSC_v3.4	4	160,988,537 - 160,988,710	UniSTS	RGSC3.4
Celera	4	146,407,705 - 146,407,878	UniSTS
RH 3.4 Map	4	1003.4	UniSTS
Cytogenetic Map	4	q42	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
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	7850904	182171018	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	23850384	169318094	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	84475257	178931073	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	86438317	168047091	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	94893247	168046938	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	105971071	168047091	Rat
1331759	Hrtrt13	Heart rate QTL 13	3.54628		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	108876717	169215811	Rat
12798519	Anxrr54	Anxiety related response QTL 54	2.54	0.05	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	112807675	157807675	Rat
724535	Cm18	Cardiac mass QTL 18	2.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	4	117926139	162926139	Rat
631683	Bp116	Blood pressure QTL 116		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	123111827	168111827	Rat
634347	Hcar8	Hepatocarcinoma resistance QTL 8	5.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	123478354	168478354	Rat
6478778	Anxrr51	Anxiety related response QTL 51		0.25384	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	123587009	168587009	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	124442168	169442168	Rat
61451	Ciaa4	CIA Autoantibody QTL 4	3.1		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	4	125884464	168047091	Rat
1358364	Sradr4	Stress Responsive Adrenal Weight QTL 4	4.92		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	128602727	173602727	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131532269	168047091	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131532269	168047091	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	131834282	176834282	Rat
1549827	Scl46	Serum cholesterol level QTL 46	3.5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	131864442	176864442	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	132455408	168047091	Rat
2303623	Vencon2	Ventilatory control QTL 2	3.8		respiration trait (VT:0001943)	minute ventilation (VE) (CMO:0000132)	4	134917642	179917642	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	136351734	174694858	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	136351734	174694858	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	136351734	180689124	Rat
2293659	Bmd35	Bone mineral density QTL 35	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	4	136908430	182878540	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	4	137171018	182171018	Rat
634342	Cia24	Collagen induced arthritis QTL 24	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	145373934	176509907	Rat
6478693	Anxrr32	Anxiety related response QTL 32		0.00092	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	145547014	184226339	Rat
6478700	Anxrr33	Anxiety related response QTL 33		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	145547014	184226339	Rat
6478718	Anxrr34	Anxiety related response QTL 34		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	145547014	184226339	Rat
6478748	Anxrr42	Anxiety related response QTL 42		0.28008	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	145547014	184226339	Rat
6478754	Anxrr43	Anxiety related response QTL 43		0.14035	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	145547014	184226339	Rat
12798525	Anxrr57	Anxiety related response QTL 57	3.21	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146086918	168047091	Rat
10401796	Kidm48	Kidney mass QTL 48			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	146497452	184226339	Rat
1582237	Kidm34	Kidney mass QTL 34	4	0.0001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	4	146942075	168998263	Rat
1581574	Eae20	Experimental allergic encephalomyelitis QTL 20	7.8		nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	152482121	158564471	Rat
6478782	Anxrr52	Anxiety related response QTL 52		0.02091	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478785	Anxrr53	Anxiety related response QTL 53		0.01397	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478720	Alc23	Alcohol consumption QTL 23		0.00509	drinking behavior trait (VT:0001422)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	155386197	184226339	Rat
6478728	Anxrr36	Anxiety related response QTL 36		0.01061	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478733	Anxrr37	Anxiety related response QTL 37		0.00095	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478737	Anxrr38	Anxiety related response QTL 38		0.00159	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478757	Anxrr44	Anxiety related response QTL 44		0.01087	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
10053718	Scort25	Serum corticosterone level QTL 25	2.15	0.0097	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	156855449	184226339	Rat
1581566	Eae21	Experimental allergic encephalomyelitis QTL 21	6.2		body mass (VT:0001259)	maximum body weight loss to initial body weight ratio (CMO:0001400)	4	157399119	158564471	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	220
Count of miRNA genes:	132
Interacting mature miRNAs:	147
Transcripts:	ENSRNOT00000021915
Prediction methods:	Microtar, 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	8	31	19	19	19			2	14	14	11
Low		25	22	18		18	8	11	72	21	24		8
Below cutoff		2	2	2		2					3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012705	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006237331	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006237333	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008763280	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039107080	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC115420	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000150	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M15768	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000021915 ⟹ ENSRNOP00000021915

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	157,383,052 - 157,408,176 (-)	Ensembl

RefSeq Acc Id:

NM_012705 ⟹ NP_036837

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	157,670,064 - 157,695,191 (-)	NCBI
Rnor_6.0	4	157,383,052 - 157,408,176 (-)	NCBI
Rnor_5.0	4	224,399,640 - 224,426,134 (-)	NCBI
RGSC_v3.4	4	160,988,512 - 161,014,038 (-)	RGD
Celera	4	146,407,680 - 146,432,465 (-)	RGD

Sequence:

show sequence

AGAAGAAAGGACTGGCCAGAGACTCAGATCCCCATCCGCTCAAGCAGGCCACCATGTGCCGAGG
CTTCTCTTTCAGGCACTTGCTGCCGCTGCTGCTCCTGCAGCTGTCAAAACTCCTAGTTGTCACC
CAAGGAAAGACCGTGGTGCTGGGGAAGGAAGGGGGTTCAGCAGAACTGCCCTGTGAAAGTACCT
CGAGGAGGAGTGCATCCTTCGCGTGGAAGTCCTCTGACCAAAAGACAATTCTGGGATATAAGAA
CAAGTTATTGATTAAAGGTTCACTTGAGCTGTATAGTCGTTTTGATTCCAGAAAAAATGCATGG
GAGAGAGGATCATTTCCCCTCATCATCAATAAACTTAGGATGGAGGACTCTCAGACTTATGTCT
GCGAGCTGGAGAACAAGAAAGAGGAGGTGGAGTTGTGGGTCTTCAGAGTGACCTTCAATCCGGG
TACCAGACTGTTGCAGGGGCAGAGCCTGACCCTGATCTTGGATAGCAACCCTAAGGTCTCTGAC
CCCCCGATAGAGTGCAAACACAAAAGCAGTAACATTGTCAAGGACTCCAAAGCTTTCTCCACGC
ACAGCCTAAGGATTCAGGACAGTGGCATCTGGAACTGCACCGTGACCCTGAACCAGAAGAAGCA
CTCATTTGACATGAAACTCTCAGTGCTGGGCTTTGCGAGCACATCCATCACGGCCTATAAGAGT
GAGGGGGAGTCAGCGGAGTTCTCCTTCCCACTCAACCTTGGAGAGGAAAGCCTGCAGGGAGAGT
TGAGATGGAAGGCAGAGAAGGCTCCTTCTTCCCAGTCCTGGATCACCTTCTCCCTAAAGAACCA
AAAGGTGTCTGTGCAGAAGTCTACTAGCAACCCCAAGTTCCAGCTGTCCGAAACGCTCCCACTC
ACCCTTCAGATACCCCAGGTCTCCCTTCAGTTTGCTGGTTCTGGCAACCTGACCCTGACTCTGG
ACAGAGGGATACTGTATCAGGAAGTGAACCTGGTGGTGATGAAAGTGACTCAGCCCGACAGCAA
CACTTTGACCTGTGAGGTGATGGGACCCACCTCACCCAAGATGAGACTGATCTTGAAGCAGGAG
AATCAGGAGGCCAGGGTCTCCAGGCAGGAGAAAGTGATTCAAGTGCAGGCCCCTGAAGCAGGGG
TGTGGCAATGTCTACTGAGTGAAGGTGAAGAGGTCAAGATGGACTCCAAGATCCAGGTTTTATC
CAAAGGGTTGAACCAGACAATGTTCCTGGCTGTCGTGCTGGGGAGCGCCTTCAGCTTTCTGGTT
TTCACGGGGCTCTGCATCCTATTCTGTGTCAGGTGCCGGCACCAACAGCGCCAGGCAGCACGGA
TGTCTCAGATCAAGAGGCTTCTCAGTGAGAAGAAGACTTGCCAGTGCTCCCACCGGATGCAGAA
AAGCCACAATCTCATATGAGGCCTGGGCCCCACCTGCAGCCCTGCCTGTGTCCTGTCGCTGACC
CAGGCCTGTGGACCAGATGAATGTAGCCCACACAGTGCCTCTGGCCTCCTGCTTTTCTCTTCCA
CAACTGGCCACGGTTTCTCTGCCTCTGTTCCCAAGCCCGTTGGCTGAGCTTGCGCTCGGCTGTG
TTTCAGACACTCAAGCACACCCAGCCAGCTTATTGATCCTCCGTAGCTGCCTTTACGCCAGAGC
CCAGCCCTTCTCTGACTAACATCCTGGATCTTCTTTCCAGCTGTCTGCTTGGATCTAAGGGCAC
CTGACCTGGATGGTGGGACTG

hide sequence

RefSeq Acc Id:

XM_006237331 ⟹ XP_006237393

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	157,668,878 - 157,695,365 (-)	NCBI
Rnor_6.0	4	157,381,862 - 157,408,355 (-)	NCBI
Rnor_5.0	4	224,399,640 - 224,426,134 (-)	NCBI

Sequence:

show sequence

AGGGACTCCTGAGGGCTGGCTCACGTCCGCCGCTGTGTAGAGGAGCCTCGCCACCAGGCTTCCT
GTCTTTTCATTTACGAACATCTGTGAAGACATAGCAAGACTGTCTTCTTCACTAGGCACCTGTC
TGCAAGGCCTCGAGCCCTCCTATAGACACACCTGTGCAAGAAGCAGAGCGAAGAAGGAAGGACT
GGCCAGAGCACCAAGTGGTCACTAGAAGACCAGGAAGCCTAAAGGACACAGCCAGTAGCAGCCA
ACTCCCTTGGTGGAATTTGGTCCTAGAACTCAGATCCCCATCCGCTCAAGCAGGCCACCATGTG
CCGAGGCTTCTCTTTCAGGCACTTGCTGCCGCTGCTGCTCCTGCAGCTGTCAAAACTCCTAGTT
GTCACCCAAGGAAAGACCGTGGTGCTGGGGAAGGAAGGGGGTTCAGCAGAACTGCCCTGTGAAA
GTACCTCGAGGAGGAGTGCATCCTTCGCGTGGAAGTCCTCTGACCAAAAGACAATTCTGGGATA
TAAGAACAAGTTATTGATTAAAGGTTCACTTGAGCTGTATAGTCGTTTTGATTCCAGAAAAAAT
GCATGGGAGAGAGGATCATTTCCCCTCATCATCAATAAACTTAGGATGGAGGACTCTCAGACTT
ATGTCTGCGAGCTGGAGAACAAGAAAGAGGAGGTGGAGTTGTGGGTCTTCAGAGTGACCTTCAA
TCCGGGTACCAGACTGTTGCAGGGGCAGAGCCTGACCCTGATCTTGGATAGCAACCCTAAGGTC
TCTGACCCCCCGATAGAGTGCAAACACAAAAGCAGTAACATTGTCAAGGACTCCAAAGCTTTCT
CCACGCACAGCCTAAGGATTCAGGACAGTGGCATCTGGAACTGCACCGTGACCCTGAACCAGAA
GAAGCACTCATTTGACATGAAACTCTCAGTGCTGGGCTTTGCGAGCACATCCATCACGGCCTAT
AAGAGTGAGGGGGAGTCAGCGGAGTTCTCCTTCCCACTCAACCTTGGAGAGGAAAGCCTGCAGG
GAGAGTTGAGATGGAAGGCAGAGAAGGCTCCTTCTTCCCAGTCCTGGATCACCTTCTCCCTAAA
GAACCAAAAGGTGTCTGTGCAGAAGTCTACTAGCAACCCCAAGTTCCAGCTGTCCGAAACGCTC
CCACTCACCCTTCAGATACCCCAGGTCTCCCTTCAGTTTGCTGGTTCTGGCAACCTGACCCTGA
CTCTGGACAGAGGGATACTGTATCAGGAAGTGAACCTGGTGGTGATGAAAGTGACTCAGCCCGA
CAGCAACACTTTGACCTGTGAGGTGATGGGACCCACCTCACCCAAGATGAGACTGATCTTGAAG
CAGGAGAATCAGGAGGCCAGGGTCTCCAGGCAGGAGAAAGTGATTCAAGTGCAGGCCCCTGAAG
CAGGGGTGTGGCAATGTCTACTGAGTGAAGGTGAAGAGGTCAAGATGGACTCCAAGATCCAGGT
TTTATCCAAAGGGTTGAACCAGACAATGTTCCTGGCTGTCGTGCTGGGGAGCGCCTTCAGCTTT
CTGGTTTTCACGGGGCTCTGCATCCTATTCTGTGTCAGGTGCCGGCACCAACAGCGCCAGGCAG
CACGGATGTCTCAGATCAAGAGGCTTCTCAGTGAGAAGAAGACTTGCCAGTGCTCCCACCGGAT
GCAGAAAAGCCACAATCTCATATGAGGCCTGGGCCCCACCTGCAGCCCTGCCTGTGTCCTGTCG
CTGACCCAGGCCTGTGGACCAGATGAATGTAGCCCACACAGTGCCTCTGGCCTCCTGCTTTTCT
CTTCCACAACTGGCCACGGTTTCTCTGCCTCTGTTCCCAAGCCCGTTGGCTGAGCTTGCGCTCG
GCTGTGTTTCAGACACTCAAGCACACCCAGCCAGCTTATTGATCCTCCGTAGCTGCCTTTACGC
CAGAGCCCAGCCCTTCTCTGACTAACATCCTGGATCTTCTTTCCAGCTGTCTGCTTGGATCTAA
GGGCACCTGACCTGGATGGTGGGACTGGTGTCTGGAAACACACAGCACAGTTCAGGAGAGACCT
CTGGGACCAGGCTGAGTGGGGGGCCTCACGCACATCACACATCCTTTCAGGGGCAGATGCAGTC
TGAGAGGGCGCGGAAGTCAGCTTCAGCTTCCCTGGCTGTCTGCTTCTTGTTTGAGGGGGCAAGA
CCAGACTCACATTCTGACCAGTTCAACAACACATGTCCAGACCACCTGCACACGGCCACACACC
TGTCCATATATCGGAACAGCATATCTTAATTCGTAAGCCAGTTTAACGTCCTGGGTGTTTGACC
CTCACAGAAACCTTACATGTGGGTTAGCAAGATGGGCTCAGTAGTAGAAAGCTCTTGCTGCCAA
GTGTGGTGACCTGAGTTCGATTCTTGAGAGCGGAAGTAGAGAATCGACTCTTGAAACCCTCATG
TGTACACCACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
GCACGGTGAAATCTTACAAGCTGACAGTGACAGCCAAGATGGCAGAGAGAACCAATCATCCCTA
GTAAAATGGAACGTGGGTTGAATGAACAAGTGCTGATGTGGGACCAACCCAGAACTTCTGATCC
CTAGAGCCTCTGTGTGAGAGACAGGGATGACCGCCACACAGAGCTCTGGAGCAAGTCCTAGGCA
CCAAGGACACACAGGAGCATAGCCCAGGCGGAGATCATGAGAGCATGGAGGAGAGCTTGTTTCA
AATCCTCCTTGACCACTGCTGTCCGGCCCTTTACCAAAGGACAAAACCCTGCTTCTCTTAGAGT
GAGGCTGGGAGAGACCCACCCCTCAGTGTGTGCAGAGCCTGGGAAGTGAGCAGTGCCGGGGTCC
TTCATGGAGAGCACTGTGGCAGGTGGCTGTACCTCCCGTCCTTCCCACACATCCGGGGAGGTCA
GGGGTCTAAGGACTCGCCCTGCTGGTCTTGATCTGTTCCTCTCAGACTCTCAGCCTCCTCTGCC
TCTTTCTGATTTCTGGCTTTAGGATCCCCTTTCCCTCTCCCAACCCCTTTCCCTGTTTTCCTAT
TTTCTTCCCAGCTGGTCTTCTAGAAACATCCCCTCCCCATTTCTCCTCATTGCTCGCTTCTTAT
TTTTGCCCACTCCCCACTCCTGCTTCCTGAGCTGACAGGAAAATAAAGGCTATAAATAAAATGC
A

hide sequence

RefSeq Acc Id:

XM_006237333 ⟹ XP_006237395

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	157,381,862 - 157,408,357 (-)	NCBI
Rnor_5.0	4	224,399,640 - 224,426,134 (-)	NCBI

Sequence:

show sequence

GGAGGGACTCCTGAGGGCTGGCTCACGTCCGCCGCTGTGTAGAGGAGCCTCGCCACCAGGCTTC
CTGTCTTTTCATTTACGAACATCTGTGAAGACATAGCAAGACTGTCTTCTTCACTAGGCACCTG
TCTGCAAGGCCTCGAGCCCTCCTATAGACACACCTGTGCAAGAAGCAGAGCGAAGAAGGAAGGA
CTGGCCAGAGACTCAGATCCCCATCCGCTCAAGCAGGCCACCATGTGCCGAGGCTTCTCTTTCA
GGCACTTGCTGCCGCTGCTGCTCCTGCAGCTGTCAAAACTCCTAGTTGTCACCCAAGGAAAGAC
CGTGGTGCTGGGGAAGGAAGGGGGTTCAGCAGAACTGCCCTGTGAAAGTACCTCGAGGAGGAGT
GCATCCTTCGCGTGGAAGTCCTCTGACCAAAAGACAATTCTGGGATATAAGAACAAGTTATTGA
TTAAAGTGACCTTCAATCCGGGTACCAGACTGTTGCAGGGGCAGAGCCTGACCCTGATCTTGGA
TAGCAACCCTAAGGTCTCTGACCCCCCGATAGAGTGCAAACACAAAAGCAGTAACATTGTCAAG
GACTCCAAAGCTTTCTCCACGCACAGCCTAAGGATTCAGGACAGTGGCATCTGGAACTGCACCG
TGACCCTGAACCAGAAGAAGCACTCATTTGACATGAAACTCTCAGTGCTGGGCTTTGCGAGCAC
ATCCATCACGGCCTATAAGAGTGAGGGGGAGTCAGCGGAGTTCTCCTTCCCACTCAACCTTGGA
GAGGAAAGCCTGCAGGGAGAGTTGAGATGGAAGGCAGAGAAGGCTCCTTCTTCCCAGTCCTGGA
TCACCTTCTCCCTAAAGAACCAAAAGGTGTCTGTGCAGAAGTCTACTAGCAACCCCAAGTTCCA
GCTGTCCGAAACGCTCCCACTCACCCTTCAGATACCCCAGGTCTCCCTTCAGTTTGCTGGTTCT
GGCAACCTGACCCTGACTCTGGACAGAGGGATACTGTATCAGGAAGTGAACCTGGTGGTGATGA
AAGTGACTCAGCCCGACAGCAACACTTTGACCTGTGAGGTGATGGGACCCACCTCACCCAAGAT
GAGACTGATCTTGAAGCAGGAGAATCAGGAGGCCAGGGTCTCCAGGCAGGAGAAAGTGATTCAA
GTGCAGGCCCCTGAAGCAGGGGTGTGGCAATGTCTACTGAGTGAAGGTGAAGAGGTCAAGATGG
ACTCCAAGATCCAGGTTTTATCCAAAGGGTTGAACCAGACAATGTTCCTGGCTGTCGTGCTGGG
GAGCGCCTTCAGCTTTCTGGTTTTCACGGGGCTCTGCATCCTATTCTGTGTCAGGTGCCGGCAC
CAACAGCGCCAGGCAGCACGGATGTCTCAGATCAAGAGGCTTCTCAGTGAGAAGAAGACTTGCC
AGTGCTCCCACCGGATGCAGAAAAGCCACAATCTCATATGAGGCCTGGGCCCCACCTGCAGCCC
TGCCTGTGTCCTGTCGCTGACCCAGGCCTGTGGACCAGATGAATGTAGCCCACACAGTGCCTCT
GGCCTCCTGCTTTTCTCTTCCACAACTGGCCACGGTTTCTCTGCCTCTGTTCCCAAGCCCGTTG
GCTGAGCTTGCGCTCGGCTGTGTTTCAGACACTCAAGCACACCCAGCCAGCTTATTGATCCTCC
GTAGCTGCCTTTACGCCAGAGCCCAGCCCTTCTCTGACTAACATCCTGGATCTTCTTTCCAGCT
GTCTGCTTGGATCTAAGGGCACCTGACCTGGATGGTGGGACTGGTGTCTGGAAACACACAGCAC
AGTTCAGGAGAGACCTCTGGGACCAGGCTGAGTGGGGGGCCTCACGCACATCACACATCCTTTC
AGGGGCAGATGCAGTCTGAGAGGGCGCGGAAGTCAGCTTCAGCTTCCCTGGCTGTCTGCTTCTT
GTTTGAGGGGGCAAGACCAGACTCACATTCTGACCAGTTCAACAACACATGTCCAGACCACCTG
CACACGGCCACACACCTGTCCATATATCGGAACAGCATATCTTAATTCGTAAGCCAGTTTAACG
TCCTGGGTGTTTGACCCTCACAGAAACCTTACATGTGGGTTAGCAAGATGGGCTCAGTAGTAGA
AAGCTCTTGCTGCCAAGTGTGGTGACCTGAGTTCGATTCTTGAGAGCGGAAGTAGAGAATCGAC
TCTTGAAACCCTCATGTGTACACCACACACACACACACACACACACACACACACACACACACAC
ACACACACACACACACGCACGGTGAAATCTTACAAGCTGACAGTGACAGCCAAGATGGCAGAGA
GAACCAATCATCCCTAGTAAAATGGAACGTGGGTTGAATGAACAAGTGCTGATGTGGGACCAAC
CCAGAACTTCTGATCCCTAGAGCCTCTGTGTGAGAGACAGGGATGACCGCCACACAGAGCTCTG
GAGCAAGTCCTAGGCACCAAGGACACACAGGAGCATAGCCCAGGCGGAGATCATGAGAGCATGG
AGGAGAGCTTGTTTCAAATCCTCCTTGACCACTGCTGTCCGGCCCTTTACCAAAGGACAAAACC
CTGCTTCTCTTAGAGTGAGGCTGGGAGAGACCCACCCCTCAGTGTGTGCAGAGCCTGGGAAGTG
AGCAGTGCCGGGGTCCTTCATGGAGAGCACTGTGGCAGGTGGCTGTACCTCCCGTCCTTCCCAC
ACATCCGGGGAGGTCAGGGGTCTAAGGACTCGCCCTGCTGGTCTTGATCTGTTCCTCTCAGACT
CTCAGCCTCCTCTGCCTCTTTCTGATTTCTGGCTTTAGGATCCCCTTTCCCTCTCCCAACCCCT
TTCCCTGTTTTCCTATTTTCTTCCCAGCTGGTCTTCTAGAAACATCCCCTCCCCATTTCTCCTC
ATTGCTCGCTTCTTATTTTTGCCCACTCCCCACTCCTGCTTCCTGAGCTGACAGGAAAATAAAG
GCTATAAATAAAATGCA

hide sequence

RefSeq Acc Id:

XM_008763280 ⟹ XP_008761502

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	157,381,862 - 157,407,160 (-)	NCBI

Sequence:

show sequence

TCTCTCTCGTTAGAATAATTAATTCTAAGAGAATTCGTCTTGGCTACAGACCCCAGTGGTCTTG
GTACAAAGTGGGCATAAGGTAGAACTCTATTTCTCAAGACAGGGTGAGCTGTTCAACTCTGGCC
CCCTGACTTCAGACCCTCAGACCTTTCTCCTCTCCTACAGCCACATGGTCTTGAAGTCCTGTTG
TACCCATGGATGATGTCCTTCAGTTCATAGACTTGTTCCCGGAGAGTGGTTTCCTGAGGTTCAG
TCTGATTCTTCATAATAGAAAGGTTCCGTCTTGATAATTCAAAAACTCTATTGAGTGGAATAGA
GGAATGTCCTGGTCTTGTAGGGAACTTTATTTATTTATTTTATTTATTTAATGTCGTAAGCAAG
GCCGGGAGAACCTGATGACAGAGACCAGTGCTGTTTCATGTTCTGACCATTTCTGGTGCTATCT
GAGATTCTGAAGGTTGATACAAAATGGCCGCCCCGCTAATGAAAGATCCCCTGAGGAGCCAGAT
ACTCAGAACCAGTTTTCCCTTTCAACCGGAGGCCCTCATAGAAGAGGCCTGCCTCTAAGTGCAA
AATCTTCCCCCACAATCAACCATACTAGGCAGAGGCTCGAAGTGGCCTTGGGTCTTGCTCTTGA
CCACAGTGGTGAAGAGGCAGTGGTTGGGAGTTGGGTGGCCATGTCTGGCATGTCTTAGACACGT
AGTAAACATTTGTTGGGTTAAATACCTTGGATGGAGATGGGAAATGTTATGATGGAGGGGAGGA
TGTGTATACGAGCATCTGTAGGGCGTGCATGTTCAGTGCTTTCAGAGACAAGAGCAGCAGGGGG
TACAGACCCCCCCACCCACTGCCACCCACCCTTTGCGCGTGGGCATCTGAGGCAGAGGAGAGGG
TGGCAGAGGTTGCAGCCACTGAACCACAAGGGTCGCTTAGAGGGTCACATCTCTAGGAAGTTTA
TACAAAGCTAGTCAGCAGAGGAAGGGTGTGTGGTGAGGGGGCACAGCCCACAACTGGGCTAGAG
TGGGCTGACTGGGGACCATGAGGAGAAGATGAAAACGCCTTCAGGACCACAGGCTGTCGTTGTG
GTGGGGCTGTGCTGGAGCTGTGCCCTCCTCTCCCATCTCTGGGGGCCCTGTGAGGGTGGCAGGA
ACCCCAAGCATCTTGAAAGACTCAGATCCCCATCCGCTCAAGCAGGCCACCATGTGCCGAGGCT
TCTCTTTCAGGCACTTGCTGCCGCTGCTGCTCCTGCAGCTGTCAAAACTCCTAGTTGTCACCCA
AGGAAAGACCGTGGTGCTGGGGAAGGAAGGGGGTTCAGCAGAACTGCCCTGTGAAAGTACCTCG
AGGAGGAGTGCATCCTTCGCGTGGAAGTCCTCTGACCAAAAGACAATTCTGGGATATAAGAACA
AGTTATTGATTAAAGGTTCACTTGAGCTGTATAGTCGTTTTGATTCCAGAAAAAATGCATGGGA
GAGAGGATCATTTCCCCTCATCATCAATAAACTTAGGATGGAGGACTCTCAGACTTATGTCTGC
GAGCTGGAGAACAAGAAAGAGGAGGTGGAGTTGTGGGTCTTCAGAGTGACCTTCAATCCGGGTA
CCAGACTGTTGCAGGGGCAGAGCCTGACCCTGATCTTGGATAGCAACCCTAAGGTCTCTGACCC
CCCGATAGAGTGCAAACACAAAAGCAGTAACATTGTCAAGGACTCCAAAGCTTTCTCCACGCAC
AGCCTAAGGATTCAGGACAGTGGCATCTGGAACTGCACCGTGACCCTGAACCAGAAGAAGCACT
CATTTGACATGAAACTCTCAGTGCTGGGCTTTGCGAGCACATCCATCACGGCCTATAAGAGTGA
GGGGGAGTCAGCGGAGTTCTCCTTCCCACTCAACCTTGGAGAGGAAAGCCTGCAGGGAGAGTTG
AGATGGAAGGCAGAGAAGGCTCCTTCTTCCCAGTCCTGGATCACCTTCTCCCTAAAGAACCAAA
AGGTGTCTGTGCAGAAGTCTACTAGCAACCCCAAGTTCCAGCTGTCCGAAACGCTCCCACTCAC
CCTTCAGATACCCCAGGTCTCCCTTCAGTTTGCTGGTTCTGGCAACCTGACCCTGACTCTGGAC
AGAGGGATACTGTATCAGGAAGTGAACCTGGTGGTGATGAAAGTGACTCAGCCCGACAGCAACA
CTTTGACCTGTGAGGTGATGGGACCCACCTCACCCAAGATGAGACTGATCTTGAAGCAGGAGAA
TCAGGAGGCCAGGGTCTCCAGGCAGGAGAAAGTGATTCAAGTGCAGGCCCCTGAAGCAGGGGTG
TGGCAATGTCTACTGAGTGAAGGTGAAGAGGTCAAGATGGACTCCAAGATCCAGGTTTTATCCA
AAGGGTTGAACCAGACAATGTTCCTGGCTGTCGTGCTGGGGAGCGCCTTCAGCTTTCTGGTTTT
CACGGGGCTCTGCATCCTATTCTGTGTCAGGTGCCGGCACCAACAGCGCCAGGCAGCACGGATG
TCTCAGATCAAGAGGCTTCTCAGTGAGAAGAAGACTTGCCAGTGCTCCCACCGGATGCAGAAAA
GCCACAATCTCATATGAGGCCTGGGCCCCACCTGCAGCCCTGCCTGTGTCCTGTCGCTGACCCA
GGCCTGTGGACCAGATGAATGTAGCCCACACAGTGCCTCTGGCCTCCTGCTTTTCTCTTCCACA
ACTGGCCACGGTTTCTCTGCCTCTGTTCCCAAGCCCGTTGGCTGAGCTTGCGCTCGGCTGTGTT
TCAGACACTCAAGCACACCCAGCCAGCTTATTGATCCTCCGTAGCTGCCTTTACGCCAGAGCCC
AGCCCTTCTCTGACTAACATCCTGGATCTTCTTTCCAGCTGTCTGCTTGGATCTAAGGGCACCT
GACCTGGATGGTGGGACTGGTGTCTGGAAACACACAGCACAGTTCAGGAGAGACCTCTGGGACC
AGGCTGAGTGGGGGGCCTCACGCACATCACACATCCTTTCAGGGGCAGATGCAGTCTGAGAGGG
CGCGGAAGTCAGCTTCAGCTTCCCTGGCTGTCTGCTTCTTGTTTGAGGGGGCAAGACCAGACTC
ACATTCTGACCAGTTCAACAACACATGTCCAGACCACCTGCACACGGCCACACACCTGTCCATA
TATCGGAACAGCATATCTTAATTCGTAAGCCAGTTTAACGTCCTGGGTGTTTGACCCTCACAGA
AACCTTACATGTGGGTTAGCAAGATGGGCTCAGTAGTAGAAAGCTCTTGCTGCCAAGTGTGGTG
ACCTGAGTTCGATTCTTGAGAGCGGAAGTAGAGAATCGACTCTTGAAACCCTCATGTGTACACC
ACACACACACACACACACACACACACACACACACACACACACACACACACACACACGCACGGTG
AAATCTTACAAGCTGACAGTGACAGCCAAGATGGCAGAGAGAACCAATCATCCCTAGTAAAATG
GAACGTGGGTTGAATGAACAAGTGCTGATGTGGGACCAACCCAGAACTTCTGATCCCTAGAGCC
TCTGTGTGAGAGACAGGGATGACCGCCACACAGAGCTCTGGAGCAAGTCCTAGGCACCAAGGAC
ACACAGGAGCATAGCCCAGGCGGAGATCATGAGAGCATGGAGGAGAGCTTGTTTCAAATCCTCC
TTGACCACTGCTGTCCGGCCCTTTACCAAAGGACAAAACCCTGCTTCTCTTAGAGTGAGGCTGG
GAGAGACCCACCCCTCAGTGTGTGCAGAGCCTGGGAAGTGAGCAGTGCCGGGGTCCTTCATGGA
GAGCACTGTGGCAGGTGGCTGTACCTCCCGTCCTTCCCACACATCCGGGGAGGTCAGGGGTCTA
AGGACTCGCCCTGCTGGTCTTGATCTGTTCCTCTCAGACTCTCAGCCTCCTCTGCCTCTTTCTG
ATTTCTGGCTTTAGGATCCCCTTTCCCTCTCCCAACCCCTTTCCCTGTTTTCCTATTTTCTTCC
CAGCTGGTCTTCTAGAAACATCCCCTCCCCATTTCTCCTCATTGCTCGCTTCTTATTTTTGCCC
ACTCCCCACTCCTGCTTCCTGAGCTGACAGGAAAATAAAGGCTATAAATAAAATGCA

hide sequence

RefSeq Acc Id:

XM_039107080 ⟹ XP_038963008

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	157,670,979 - 157,695,366 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_036837	(Get FASTA)	NCBI Sequence Viewer
	XP_006237393	(Get FASTA)	NCBI Sequence Viewer
	XP_038963008	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40901	(Get FASTA)	NCBI Sequence Viewer
	EDM01911	(Get FASTA)	NCBI Sequence Viewer
	EDM01912	(Get FASTA)	NCBI Sequence Viewer
	EDM01913	(Get FASTA)	NCBI Sequence Viewer
	P05540	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_036837 ⟸ NM_012705
- Peptide Label:	precursor
- UniProtKB:	P05540 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MCRGFSFRHLLPLLLLQLSKLLVVTQGKTVVLGKEGGSAELPCESTSRRSASFAWKSSDQKTIL GYKNKLLIKGSLELYSRFDSRKNAWERGSFPLIINKLRMEDSQTYVCELENKKEEVELWVFRVT FNPGTRLLQGQSLTLILDSNPKVSDPPIECKHKSSNIVKDSKAFSTHSLRIQDSGIWNCTVTLN QKKHSFDMKLSVLGFASTSITAYKSEGESAEFSFPLNLGEESLQGELRWKAEKAPSSQSWITFS LKNQKVSVQKSTSNPKFQLSETLPLTLQIPQVSLQFAGSGNLTLTLDRGILYQEVNLVVMKVTQ PDSNTLTCEVMGPTSPKMRLILKQENQEARVSRQEKVIQVQAPEAGVWQCLLSEGEEVKMDSKI QVLSKGLNQTMFLAVVLGSAFSFLVFTGLCILFCVRCRHQQRQAARMSQIKRLLSEKKTCQCSH RMQKSHNLI hide sequence

RefSeq Acc Id:

XP_006237395 ⟸ XM_006237333

- Peptide Label:

isoform X2

- Sequence:

show sequence

MCRGFSFRHLLPLLLLQLSKLLVVTQGKTVVLGKEGGSAELPCESTSRRSASFAWKSSDQKTIL
GYKNKLLIKVTFNPGTRLLQGQSLTLILDSNPKVSDPPIECKHKSSNIVKDSKAFSTHSLRIQD
SGIWNCTVTLNQKKHSFDMKLSVLGFASTSITAYKSEGESAEFSFPLNLGEESLQGELRWKAEK
APSSQSWITFSLKNQKVSVQKSTSNPKFQLSETLPLTLQIPQVSLQFAGSGNLTLTLDRGILYQ
EVNLVVMKVTQPDSNTLTCEVMGPTSPKMRLILKQENQEARVSRQEKVIQVQAPEAGVWQCLLS
EGEEVKMDSKIQVLSKGLNQTMFLAVVLGSAFSFLVFTGLCILFCVRCRHQQRQAARMSQIKRL
LSEKKTCQCSHRMQKSHNLI

hide sequence

RefSeq Acc Id:	XP_006237393 ⟸ XM_006237331
- Peptide Label:	isoform X1
- UniProtKB:	P05540 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MCRGFSFRHLLPLLLLQLSKLLVVTQGKTVVLGKEGGSAELPCESTSRRSASFAWKSSDQKTIL GYKNKLLIKGSLELYSRFDSRKNAWERGSFPLIINKLRMEDSQTYVCELENKKEEVELWVFRVT FNPGTRLLQGQSLTLILDSNPKVSDPPIECKHKSSNIVKDSKAFSTHSLRIQDSGIWNCTVTLN QKKHSFDMKLSVLGFASTSITAYKSEGESAEFSFPLNLGEESLQGELRWKAEKAPSSQSWITFS LKNQKVSVQKSTSNPKFQLSETLPLTLQIPQVSLQFAGSGNLTLTLDRGILYQEVNLVVMKVTQ PDSNTLTCEVMGPTSPKMRLILKQENQEARVSRQEKVIQVQAPEAGVWQCLLSEGEEVKMDSKI QVLSKGLNQTMFLAVVLGSAFSFLVFTGLCILFCVRCRHQQRQAARMSQIKRLLSEKKTCQCSH RMQKSHNLI hide sequence

RefSeq Acc Id:

XP_008761502 ⟸ XM_008763280

- Peptide Label:

isoform X1

- Sequence:

show sequence

MCRGFSFRHLLPLLLLQLSKLLVVTQGKTVVLGKEGGSAELPCESTSRRSASFAWKSSDQKTIL
GYKNKLLIKGSLELYSRFDSRKNAWERGSFPLIINKLRMEDSQTYVCELENKKEEVELWVFRVT
FNPGTRLLQGQSLTLILDSNPKVSDPPIECKHKSSNIVKDSKAFSTHSLRIQDSGIWNCTVTLN
QKKHSFDMKLSVLGFASTSITAYKSEGESAEFSFPLNLGEESLQGELRWKAEKAPSSQSWITFS
LKNQKVSVQKSTSNPKFQLSETLPLTLQIPQVSLQFAGSGNLTLTLDRGILYQEVNLVVMKVTQ
PDSNTLTCEVMGPTSPKMRLILKQENQEARVSRQEKVIQVQAPEAGVWQCLLSEGEEVKMDSKI
QVLSKGLNQTMFLAVVLGSAFSFLVFTGLCILFCVRCRHQQRQAARMSQIKRLLSEKKTCQCSH
RMQKSHNLI

hide sequence

RefSeq Acc Id:

ENSRNOP00000021915 ⟸ ENSRNOT00000021915

RefSeq Acc Id:	XP_038963008 ⟸ XM_039107080
- Peptide Label:	isoform X2

Protein Domains

Ig-like C2-type Ig-like V-type

Transcriptome

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

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:2306	AgrOrtholog
Ensembl Genes	ENSRNOG00000016294	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000021915	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000021915	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.10	UniProtKB/Swiss-Prot
InterPro	CD4	UniProtKB/Swiss-Prot
	CD4-extracel	UniProtKB/Swiss-Prot
	Ig-like_dom	UniProtKB/Swiss-Prot
	Ig-like_dom_sf	UniProtKB/Swiss-Prot
	Ig-like_fold	UniProtKB/Swiss-Prot
	Ig_C2-set	UniProtKB/Swiss-Prot
	Ig_sub	UniProtKB/Swiss-Prot
	Ig_V-set	UniProtKB/Swiss-Prot
	Immunoglobulin	UniProtKB/Swiss-Prot
	Tcell_CD4_Cterm	UniProtKB/Swiss-Prot
KEGG Report	rno:24932	UniProtKB/Swiss-Prot
NCBI Gene	24932	ENTREZGENE
PANTHER	PTHR11422:SF0	UniProtKB/Swiss-Prot
Pfam	C2-set	UniProtKB/Swiss-Prot
	CD4-extracel	UniProtKB/Swiss-Prot
	PF00047	UniProtKB/Swiss-Prot
	Tcell_CD4_C	UniProtKB/Swiss-Prot
PhenoGen	Cd4	PhenoGen
PRINTS	CD4TCANTIGEN	UniProtKB/Swiss-Prot
PROSITE	IG_LIKE	UniProtKB/Swiss-Prot
SMART	IGv	UniProtKB/Swiss-Prot
	SM00409	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF48726	UniProtKB/Swiss-Prot
UniProt	CD4_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-29	Cd4	Cd4 molecule	Cd4	CD4 antigen	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-11-06	Cd4	CD4 antigen		CD4 antigen (p55)	Name updated	625702	APPROVED
2002-06-10	Cd4	CD4 antigen (p55)			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_process	has a role as receptor necessary for HIV infection in humans	632390

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 - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)