Cd74 (CD74 molecule) - Rat Genome Database

Name: Cd74
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Cd74 (CD74 molecule) Rattus norvegicus

Analyze

Symbol:

Cd74

Name:

CD74 molecule

RGD ID:

2313

Description:

Is predicted to contribute to cytokine binding activity. Involved in activation of MAPK activity and cell population proliferation. Predicted to colocalize with MHC class II protein complex. Orthologous to human CD74 (CD74 molecule); PARTICIPATES IN antigen processing and presentation pathway; tuberculosis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

CD74 antigen (invariant polpypeptide of major histocompatibility class II antigen-associated); CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated); Cd74 molecule, major histocompatibility complex, class II invariant chain; H-2 class II histocompatibility antigen gamma chain; ia antigen-associated invariant chain; ii; INVG34; MHC class II-associated invariant chain

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

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	18	54,256,757 - 54,266,003 (+)	NCBI
Rnor_6.0 Ensembl	18	56,071,478 - 56,080,849 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	56,071,420 - 56,080,851 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	55,305,827 - 55,315,246 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	56,756,511 - 56,765,711 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	56,828,786 - 56,837,940 (+)	NCBI
Celera	18	52,411,586 - 52,420,786 (+)	NCBI		Celera
RH 3.4 Map	18	525.0	RGD
Cytogenetic Map	18	q12.1	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Acute Liver Failure (ISO)

Breast Neoplasms (ISO)

Experimental Liver Cirrhosis (ISO)

Hereditary Neoplastic Syndromes (ISO)

lung non-small cell carcinoma (ISO)

Treacher Collins syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (EXP)

17beta-estradiol 3-benzoate (EXP)

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

2-nitrofluorene (EXP)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (EXP)

7,12-dimethyltetraphene (ISO)

8-Br-cAMP (ISO)

acetamide (EXP)

acetylsalicylic acid (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

amitriptyline (EXP)

ammonium chloride (EXP)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzene (EXP)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

Benzo[k]fluoranthene (ISO)

bergomottin (ISO)

bexarotene (EXP)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

bupropion (ISO)

buspirone (EXP)

captan (ISO)

carbon nanotube (ISO)

carbonyl sulfide (EXP)

choline (ISO)

ciguatoxin CTX1B (ISO)

clofibrate (ISO)

clothianidin (ISO)

cocaine (EXP)

copper atom (EXP)

copper(0) (EXP)

cyclophosphamide (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

diarsenic trioxide (ISO)

diethylstilbestrol (ISO)

dioxygen (ISO)

diuron (EXP)

doramapimod (ISO)

dorsomorphin (ISO)

doxorubicin (EXP,ISO)

elemental selenium (ISO)

entinostat (ISO)

ethanol (ISO)

ferric oxide (ISO)

folpet (ISO)

genistein (ISO)

gentamycin (EXP)

glycidol (EXP)

hexachlorobenzene (EXP)

hydroxychloroquine (ISO)

iron atom (ISO)

iron(0) (ISO)

isoprenaline (ISO)

lead(0) (ISO)

lead(2+) (ISO)

losartan (EXP)

luteolin (ISO)

manganese(II) chloride (EXP)

menadione (ISO)

metformin (EXP)

methotrexate (ISO)

N-(6-acetamidohexyl)acetamide (ISO)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

N-nitrosomorpholine (EXP)

n-propyl gallate (EXP)

nefazodone (EXP)

nickel sulfate (ISO)

nimesulide (EXP)

nobiletin (ISO)

ochratoxin A (EXP)

oxaliplatin (EXP)

panobinostat (ISO)

paracetamol (ISO)

pevonedistat (ISO)

phenformin (EXP)

phenobarbital (EXP)

PhIP (EXP)

pirinixic acid (EXP,ISO)

potassium chromate (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

quercetin (ISO)

quercitrin (ISO)

raloxifene (EXP)

resveratrol (ISO)

rotenone (EXP)

SB 431542 (ISO)

selenium atom (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sodium dichromate (ISO)

sodium tungstate (ISO)

succimer (ISO)

sulfasalazine (ISO)

sulforaphane (ISO)

tacrolimus hydrate (ISO)

tamibarotene (ISO)

testosterone (EXP)

tetrachloromethane (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

toluene (EXP)

topotecan (EXP)

trichloroethene (EXP)

trichostatin A (ISO)

trimethoprim (ISO)

triphenyl phosphate (EXP)

triptonide (ISO)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (ISO)

vancomycin (ISO)

vinclozolin (EXP)

vorinostat (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of MAPK activity (IDA)

antigen processing and presentation (IBA,ISO)

antigen processing and presentation of exogenous peptide antigen via MHC class II (ISO)

cell population proliferation (IDA)

chaperone cofactor-dependent protein refolding (ISO)

defense response (ISO)

I-kappaB kinase/NF-kappaB signaling (ISO)

immunoglobulin mediated immune response (ISO)

intracellular protein transport (ISO)

macrophage migration inhibitory factor signaling pathway (ISO,ISS)

negative regulation of apoptotic process (ISO,ISS)

negative regulation of cell migration (ISO)

negative regulation of DNA damage response, signal transduction by p53 class mediator (IBA,ISO,ISS)

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (IBA,ISO,ISS)

negative regulation of mature B cell apoptotic process (ISO,ISS)

negative regulation of peptide secretion (ISO)

negative regulation of T cell differentiation (ISO)

negative regulation of viral entry into host cell (ISO)

negative thymic T cell selection (ISO)

positive regulation of B cell proliferation (ISO)

positive regulation of chemokine (C-X-C motif) ligand 2 production (ISO,ISS)

positive regulation of chemokine production (ISO)

positive regulation of cytokine production involved in inflammatory response (ISO)

positive regulation of cytokine-mediated signaling pathway (IBA,ISO,ISS)

positive regulation of dendritic cell antigen processing and presentation (ISO,ISS)

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

positive regulation of fibroblast proliferation (ISO)

positive regulation of gene expression (ISO)

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

positive regulation of inflammatory response (ISO)

positive regulation of interleukin-6 production (ISO)

positive regulation of interleukin-8 production (ISO)

positive regulation of kinase activity (IBA,ISO)

positive regulation of macrophage cytokine production (IBA,ISO,ISS)

positive regulation of macrophage migration inhibitory factor signaling pathway (ISO)

positive regulation of MAPK cascade (ISO)

positive regulation of monocyte differentiation (ISO)

positive regulation of neutrophil chemotaxis (ISO,ISS)

positive regulation of NIK/NF-kappaB signaling (ISO)

positive regulation of peptidyl-tyrosine phosphorylation (IBA,ISO,ISS)

positive regulation of prostaglandin biosynthetic process (ISO)

positive regulation of protein phosphorylation (ISO)

positive regulation of T cell differentiation (ISO)

positive regulation of transcription, DNA-templated (ISO)

positive regulation of type 2 immune response (IBA,ISO)

positive regulation of viral entry into host cell (ISO)

positive thymic T cell selection (ISO)

prostaglandin biosynthetic process (ISO,ISS)

protein stabilization (ISO,ISS)

protein trimerization (IEA)

protein-containing complex assembly (ISO)

response to interferon-gamma (ISO)

signal transduction involved in regulation of gene expression (ISO)

T cell activation involved in immune response (IBA)

Cellular Component

cell surface (IBA,ISO)

cytoplasm (IBA,ISO)

endoplasmic reticulum (ISO)

endoplasmic reticulum membrane (IEA)

external side of plasma membrane (ISO)

extracellular space (ISO)

Golgi apparatus (ISO)

integral component of membrane (ISO,TAS)

late endosome (ISO,ISS)

lysosome (ISO,ISS)

macrophage migration inhibitory factor receptor complex (ISO,ISS)

MHC class II protein complex (IBA,ISO)

multivesicular body (ISO)

NOS2-CD74 complex (ISO,ISS)

nucleus (ISO)

plasma membrane (ISO)

protein-containing complex (ISO)

vacuole (ISO)

Molecular Function

amyloid-beta binding (ISO)

CD4 receptor binding (ISO)

cytokine binding (ISO,ISS)

cytokine receptor activity (IBA,ISO,ISS)

macrophage migration inhibitory factor binding (IBA,ISO)

MHC class II protein binding (IBA,ISO)

MHC class II protein binding, via antigen binding groove (ISO)

MHC class II protein complex binding (ISO)

nitric-oxide synthase binding (ISO,ISS)

protein binding (ISO)

protein folding chaperone (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

antigen processing and presentation pathway (IEA)

tuberculosis pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Henkes W, etal., Nucleic Acids Res 1988 Dec 23;16(24):11822.
3.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
4.	Leng L, etal., J Exp Med 2003 Jun 2;197(11):1467-76.
5.	Meyer-Siegler KL and Vera PL, J Urol 2005 Feb;173(2):615-20.
6.	MGD data from the GO Consortium
7.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	Pipeline to import KEGG annotations from KEGG into RGD
9.	RGD automated import pipeline for gene-chemical interactions
10.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
11.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Additional References at PubMed

PMID:1448172	PMID:2499873	PMID:3864916	PMID:7477400	PMID:7679955	PMID:7985028	PMID:8098731	PMID:8294875	PMID:8598040	PMID:9432982	PMID:11754812	PMID:11823488
PMID:11854359	PMID:15294975	PMID:15322158	PMID:17045821	PMID:17567581	PMID:18003616	PMID:18056708	PMID:19325914	PMID:19413900	PMID:19423618	PMID:19503733	PMID:19665027
PMID:19723499	PMID:19849849	PMID:19946888	PMID:20198449	PMID:20458337	PMID:21802455	PMID:22952837	PMID:23736979	PMID:24569872	PMID:24942581	PMID:24974304	PMID:27926507
PMID:31197516

Genomics

Comparative Map Data

Cd74
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	18	54,256,757 - 54,266,003 (+)	NCBI
Rnor_6.0 Ensembl	18	56,071,478 - 56,080,849 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	56,071,420 - 56,080,851 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	55,305,827 - 55,315,246 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	56,756,511 - 56,765,711 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	56,828,786 - 56,837,940 (+)	NCBI
Celera	18	52,411,586 - 52,420,786 (+)	NCBI		Celera
RH 3.4 Map	18	525.0	RGD
Cytogenetic Map	18	q12.1	NCBI

CD74
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	150,400,041 - 150,412,969 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	5	150,400,041 - 150,412,929 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	150,400,041 - 150,412,936 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	149,779,604 - 149,792,499 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	149,761,393 - 149,772,525 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	149,761,396 - 149,772,511	NCBI
Celera	5	145,862,277 - 145,873,409 (-)	NCBI
Cytogenetic Map	5	q33.1	NCBI
HuRef	5	144,928,781 - 144,940,080 (-)	NCBI		HuRef
CHM1_1	5	149,213,619 - 149,224,915 (-)	NCBI		CHM1_1

Cd74
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	60,936,921 - 60,945,724 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	18	60,936,920 - 60,945,724 (+)	Ensembl
GRCm38	18	60,803,849 - 60,812,652 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	60,803,848 - 60,812,652 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	60,963,503 - 60,972,306 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	18	60,929,247 - 60,938,021 (+)	NCBI			mm8
Celera	18	62,088,874 - 62,098,436 (+)	NCBI		Celera
Cytogenetic Map	18	E1	NCBI
cM Map	18	34.41	NCBI

Cd74
(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_004955415	4,129,254 - 4,137,826 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955415	4,129,151 - 4,138,336 (+)	NCBI	ChiLan1.0	ChiLan1.0

CD74
(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	5	151,830,311 - 151,841,334 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	151,830,311 - 151,841,334 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	145,825,635 - 145,836,916 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CD74
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	58,689,745 - 58,698,421 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	58,689,752 - 58,698,151 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	58,456,154 - 58,464,833 (+)	NCBI
ROS_Cfam_1.0	4	59,170,613 - 59,179,292 (+)	NCBI
UMICH_Zoey_3.1	4	58,959,149 - 58,967,827 (+)	NCBI
UNSW_CanFamBas_1.0	4	59,073,563 - 59,082,236 (+)	NCBI
UU_Cfam_GSD_1.0	4	59,604,607 - 59,613,287 (+)	NCBI

Cd74
(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_024407213	142,948,591 - 142,958,314 (+)	NCBI
SpeTri2.0	NW_004936504	4,522,576 - 4,532,289 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CD74
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	2	151,402,210 - 151,409,924 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

CD74
(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	23	53,008,802 - 53,022,953 (-)	NCBI
ChlSab1.1 Ensembl	23	53,009,394 - 53,022,923 (-)	Ensembl

Cd74
(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_004624774	9,699,876 - 9,708,871 (-)	NCBI

Position Markers

RH94596

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	56,080,656 - 56,080,801	NCBI	Rnor6.0
Rnor_5.0	18	55,315,051 - 55,315,196	UniSTS	Rnor5.0
RGSC_v3.4	18	56,765,516 - 56,765,661	UniSTS	RGSC3.4
Celera	18	52,420,591 - 52,420,736	UniSTS
RH 3.4 Map	18	525.0	UniSTS
Cytogenetic Map	18	q12.1	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
2299160	Iddm35	Insulin dependent diabetes mellitus QTL 35	2.79		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	18	4407513	62570466	Rat
2313082	Bss85	Bone structure and strength QTL 85	0.8	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	18	14678852	59678852	Rat
1358358	Sradr6	Stress Responsive Adrenal Weight QTL 6	2.49		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	18	15539427	61499684	Rat
6903359	Bp355	Blood pressure QTL 355	3.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539671	61985648	Rat
2293708	Bss46	Bone structure and strength QTL 46	8.8	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	18	15695872	68524999	Rat
1578661	Bss20	Bone structure and strength QTL 20	3.7		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	18	15695872	87080053	Rat
1578667	Bss21	Bone structure and strength QTL 21	3.5		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	18	15695872	87080053	Rat
1358193	Emca2	Estrogen-induced mammary cancer QTL 2	1.6		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	18	19031030	68436105	Rat
1600373	Mamtr6	Mammary tumor resistance QTL 6			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	18	20285758	87080053	Rat
7387267	Uae42	Urinary albumin excretion QTL 42		0.61	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	14	21639491	66639491	Rat
1331741	Bp232	Blood pressure QTL 232	3.59112		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22603736	87074531	Rat
6903353	Bp353	Blood pressure QTL 353	2.8		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22604764	61985648	Rat
1331733	Bp233	Blood pressure QTL 233	3.97196		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	25961026	81761656	Rat
2300157	Bmd66	Bone mineral density QTL 66	13.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2300177	Bmd65	Bone mineral density QTL 65	19.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2293704	Bss35	Bone structure and strength QTL 35	4.59	0.0002	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	18	30533614	75533614	Rat
9590318	Scort22	Serum corticosterone level QTL 22	7.64	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	18	31361341	76361341	Rat
1331754	Bp230	Blood pressure QTL 230	4.61609		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	31361341	76361341	Rat
9589816	Gluco68	Glucose level QTL 68	7.25	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	18	31361341	76361341	Rat
8694378	Bw157	Body weight QTL 157	3.59	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	18	31361341	76361341	Rat
738005	Anxrr11	Anxiety related response QTL 11	3.4		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	18	31608424	76608424	Rat
61383	Bp47	Blood pressure QTL 47	17.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	31728373	62570429	Rat
1331776	Bp225	Blood pressure QTL 225	2.829		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	32670352	61985812	Rat
1331774	Bp226	Blood pressure QTL 226	4.41065		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331742	Bp228	Blood pressure QTL 228	3.88752		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331798	Bp224	Blood pressure QTL 224	3.53873		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331727	Bp237	Blood pressure QTL 237	3.053		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	63897621	Rat
61429	Cia17	Collagen induced arthritis QTL 17	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	18	32670352	73016546	Rat
2303120	Mamtr8	Mammary tumor resistance QTL 8		0.001	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	18	32670352	87080053	Rat
6903347	Bp350	Blood pressure QTL 350	4.4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670473	61985648	Rat
631274	Sprol1	Serum protein level QTL 1	5.3		blood total protein amount (VT:0005567)	serum total protein level (CMO:0000661)	18	32704022	80696226	Rat
631518	Bw11	Body weight QTL 11	2.8		body mass (VT:0001259)	body weight (CMO:0000012)	18	38221919	83221919	Rat
61367	Iddm4	Insulin dependent diabetes mellitus QTL 4	2.33	0.0074	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	18	40375769	85375769	Rat
6893683	Bw110	Body weight QTL 110	2.7	0.002	body mass (VT:0001259)	body weight (CMO:0000012)	18	45002194	88201929	Rat
1598826	Anxrr20	Anxiety related response QTL 20	3.04		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	18	46319476	88201929	Rat
1331806	Bp229	Blood pressure QTL 229	4.36484		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	48248877	59473805	Rat
1331736	Bp227	Blood pressure QTL 227	2.791		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	48248877	61985812	Rat
1331780	Bp238	Blood pressure QTL 238	3.269		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	48248877	61985812	Rat
6903345	Bp349	Blood pressure QTL 349	3.9		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	48249048	61985648	Rat
6903349	Bp351	Blood pressure QTL 351	3.5		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	48249048	61985648	Rat
6903351	Bp352	Blood pressure QTL 352	3.3		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	48249048	61985648	Rat
61360	Eaey	Experimental allergic encephalomyelitis QTL y	3		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis duration (CMO:0001424)	18	48519299	62570427	Rat
9589041	Epfw12	Epididymal fat weight QTL 12	17.08	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	18	49130920	88201929	Rat
8694432	Bw165	Body weight QTL 165	3.81	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	18	49130920	88201929	Rat
8694366	Abfw8	Abdominal fat weight QTL 8	6.38	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	18	49130920	88201929	Rat
2303571	Bw92	Body weight QTL 92	3		body mass (VT:0001259)	body weight (CMO:0000012)	18	51375816	88201929	Rat
2303584	Gluco55	Glucose level QTL 55	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	18	51375816	88201929	Rat
7411719	Strs5	Sensitivity to stroke QTL 5	9.4		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	18	51609032	67502266	Rat
2293658	Bmd23	Bone mineral density QTL 23	7.3	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	18	53033494	68524999	Rat
738008	Hcar14	Hepatocarcinoma resistance QTL 14	4.3		liver integrity trait (VT:0010547)	liver nonremodeling tumorous lesion number (CMO:0001462)	18	53033494	87080053	Rat
1331730	Scl27	Serum cholesterol level QTL 27	3.826		blood HDL cholesterol amount (VT:0000184)	serum high density lipoprotein cholesterol level (CMO:0000361)	18	53861252	61985812	Rat
1331752	Bw27	Body weight QTL 27	2.963		body mass (VT:0001259)	body weight (CMO:0000012)	18	53861252	67502266	Rat
1359020	Ppulsi2	Prepulse inhibition QTL 2	2.71		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	18	53861252	77151443	Rat
1600375	Mcs22	Mammary carcinoma susceptibility QTL 22	3.3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	18	54108375	68819562	Rat
631509	Sald2	Serum aldosterone level QTL 2	2.9		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	18	54108375	71692768	Rat
2301417	Bp319	Blood pressure QTL 319		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	54108375	79575348	Rat
12880368	Bw187	Body weight QTL 187		0.045	body mass (VT:0001259)	body weight (CMO:0000012)	18	54108375	79575348	Rat
12904067	Cm122	Cardiac mass QTL 122		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	18	54108375	79575348	Rat
12904069	Cm123	Cardiac mass QTL 123		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	18	54108375	79575348	Rat
12904070	Cm124	Cardiac mass QTL 124		0.01	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	18	54108375	79575348	Rat
12904071	Am18	Aortic mass QTL 18		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	18	54108375	79575348	Rat
12904073	Kidm71	Kidney mass QTL 71		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	54108375	79575348	Rat
1300125	Rf26	Renal function QTL 26	3.2		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	18	54108474	67502122	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	418
Count of miRNA genes:	133
Interacting mature miRNAs:	145
Transcripts:	ENSRNOT00000025344, ENSRNOT00000025354
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	3		5		16							5
Medium	1	25	34	23	3	23	8	11	15	25	31	6	8
Low		18	16	16		16			37	10	10
Below cutoff			2	2		2			20

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_013069	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006254761	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC095289	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC059152	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB611598	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB696567	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473971	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219430	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225098	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225326	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225666	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227357	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227455	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227561	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228116	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230327	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ231756	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232412	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232423	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232867	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232996	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233568	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233706	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234457	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000301	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X13044	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000025344 ⟹ ENSRNOP00000025342

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	56,071,478 - 56,080,849 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000025354 ⟹ ENSRNOP00000025354

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	56,071,574 - 56,080,397 (+)	Ensembl

RefSeq Acc Id:

NM_013069 ⟹ NP_037201

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	54,256,803 - 54,266,003 (+)	NCBI
Rnor_6.0	18	56,071,478 - 56,080,851 (+)	NCBI
Rnor_5.0	18	55,305,827 - 55,315,246 (+)	NCBI
RGSC_v3.4	18	56,756,511 - 56,765,711 (+)	RGD
Celera	18	52,411,586 - 52,420,786 (+)	RGD

Sequence:

show sequence

CGGGGCTCAAGGGTCCCAGATACACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCAGC
AGCACTTGGGGGAAAAGCTAGAGGCTAGAGTCATGGATGACCAGCGCGACCTCATCTCTAACCA
TGAGCAGCTGCCCATCCTGGGCCAGCGTGCTAGAGCCCCAGAAAGCAATTGCAACCGTGGAGTC
CTGTACACCAGTGTCTCTGTCCTGGTGGCTCTGCTCTTGGCTGGGCAGGCCACCACTGCTTACT
TCCTGTACCAGCAGCAGGGCCGCCTGGACAAGCTGACCGTCACCTCCCAGAACCTGCAACTGGA
GAACCTTCGCATGAAGCTTCCGAAATCTGCCAAACCTGTGAGCCCGATGCGCATGGCTACTCCC
TTGCTGATGCGCCCACTGTCCATGGATAACATGCTCCAAGCGCCCGTGAAGAATGTTACCAAGT
ATGGCAACATGACCCAGGACCACGTGATGCACCTGCTTACGAAGTCTGGACCCGTGAACTACCC
ACAGCTGAAGGGGAGCTTCCCGGAGAATCTGAAGCACCTTAAGAACTCTATGAATGGTCTGGAC
TGGAAGGTCTTTGAGAGCTGGATGAAACAGTGGCTGTTGTTTGAAATGAGCAAGAACTCCCTGG
AGGAGAAGCAGCCCACCCAGACTCCACCTAAAGAGCCACTGGACATGGAAGACCCATCTTCTGG
CCTGGGAGTGACCAAGCAGGATATGGGCCAAATGTTCTTGTGAAGACAGAAGCCAGCTCTGCAC
GGCGGCAGCTCCCCTGCTCCTCAGCCCTTCTTACACTCCCTAACATCACACCCCATTTCCCGTC
TTCCTGCACCCTGGGGCTTGAGACTGGTATCTGCTTCACCGTCCCTGGACACAACAAATGAAAC
CGGAACAGAATGAGAACACTGGAGGGAGGGCCTTGCTGCCTACCCCCATCTAAGGGACCCCCAT
TTCTGACCCATTAGCAGTCTTTAATGTGGGGCTCTGAGATCTAGGCCCACTGACAGGGATAGGG
GATGCCCTACCCTTAATCTAGGCTGGATACATTTGCTGTCTTCTCAAGGAAGAGGCCAAGCCCT
CCCAGCAACCCTTCCTCATGTCCTGCCGACGCCCCTGGGATCCCTGCTCAGCCAAGCTTGTCAG
CAGCCTGTAGGACCATGGTTCACGTGACAATAAAAGGTAGAAGGTAGAAAAAAAAAAAAAAAAA
AAAA

hide sequence

RefSeq Acc Id:

XM_006254761 ⟹ XP_006254823

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	54,256,757 - 54,266,003 (+)	NCBI
Rnor_6.0	18	56,071,420 - 56,080,851 (+)	NCBI
Rnor_5.0	18	55,305,827 - 55,315,246 (+)	NCBI

Sequence:

show sequence

GAGTGACCTGCTGTGGACGAATCAGATTCCTCCCAGTATCAGCTTCAAGAGGTGATCCCGGGGC
TCAAGGGTCCCAGATACACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCAGCAGCACT
TGGGGGAAAAGCTAGAGGCTAGAGTCATGGATGACCAGCGCGACCTCATCTCTAACCATGAGCA
GCTGCCCATCCTGGGCCAGCGTGCTAGAGCCCCAGAAAGCAATTGCAACCGTGGAGTCCTGTAC
ACCAGTGTCTCTGTCCTGGTGGCTCTGCTCTTGGCTGGGCAGGCCACCACTGCTTACTTCCTGT
ACCAGCAGCAGGGCCGCCTGGACAAGCTGACCGTCACCTCCCAGAACCTGCAACTGGAGAACCT
TCGCATGAAGCTTCCGAAATCTGCCAAACCTGTGAGCCCGATGCGCATGGCTACTCCCTTGCTG
ATGCGCCCACTGTCCATGGATAACATGCTCCAAGCGCCCGTGAAGAATGTTACCAAGTATGGCA
ACATGACCCAGGACCACGTGATGCACCTGCTTACGAAGTCTGGACCCGTGAACTACCCACAGCT
GAAGGGGAGCTTCCCGGAGAATCTGAAGCACCTTAAGAACTCTATGAATGGTCTGGACTGGAAG
GTCTTTGAGAGCTGGATGAAACAGTGGCTGTTGTTTGAAATGAGCAAGAACTCCCTGGAGGAGA
AGCAGCCCACCCAGACTCCACCTAAAGTATTGACCAAGTGCCAGGAAGAAGTCAGCCACATCCC
TGATGTCCACCCGGGGGCGTTCCGTCCCAAGTGTGATGAGAACGGTAACTATATGCCACTCCAG
TGCCATGGGAGCACTGGCTACTGCTGGTGTGTGTTCCCCAACGGCACTGAGGTCCCTCACACCA
AGAGCCGCGGGCGCCATAACTGCAGTGAGCCACTGGACATGGAAGACCCATCTTCTGGCCTGGG
AGTGACCAAGCAGGATATGGGCCAAATGTTCTTGTGAAGACAGAAGCCAGCTCTGCACGGCGGC
AGCTCCCCTGCTCCTCAGCCCTTCTTACACTCCCTAACATCACACCCCATTTCCCGTCTTCCTG
CACCCTGGGGCTTGAGACTGGTATCTGCTTCACCGTCCCTGGACACAACAAATGAAACCGGAAC
AGAATGAGAACACTGGAGGGAGGGCCTTGCTGCCTACCCCCATCTAAGGGACCCCCATTTCTGA
CCCATTAGCAGTCTTTAATGTGGGGCTCTGAGATCTAGGCCCACTGACAGGGATAGGGGATGCC
CTACCCTTAATCTAGGCTGGATACATTTGCTGTCTTCTCAAGGAAGAGGCCAAGCCCTCCCAGC
AACCCTTCCTCATGTCCTGCCGACGCCCCTGGGATCCCTGCTCAGCCAAGCTTGTCAGCAGCCT
GTAGGACCATGGTTCACGTGACAATAAAAGGTAGAAGGTAGAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_037201	(Get FASTA)	NCBI Sequence Viewer
	XP_006254823	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH59152	(Get FASTA)	NCBI Sequence Viewer
	CAA31450	(Get FASTA)	NCBI Sequence Viewer
	EDM14561	(Get FASTA)	NCBI Sequence Viewer
	EDM14562	(Get FASTA)	NCBI Sequence Viewer
	EDM14563	(Get FASTA)	NCBI Sequence Viewer
	EDM14564	(Get FASTA)	NCBI Sequence Viewer
	EDM14565	(Get FASTA)	NCBI Sequence Viewer
	EDM14566	(Get FASTA)	NCBI Sequence Viewer
	EDM14567	(Get FASTA)	NCBI Sequence Viewer
	EDM14568	(Get FASTA)	NCBI Sequence Viewer
	EDM14569	(Get FASTA)	NCBI Sequence Viewer
	P10247	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_037201 ⟸ NM_013069

- UniProtKB:

P10247 (UniProtKB/Swiss-Prot), Q6GT70 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDDQRDLISNHEQLPILGQRARAPESNCNRGVLYTSVSVLVALLLAGQATTAYFLYQQQGRLDK
LTVTSQNLQLENLRMKLPKSAKPVSPMRMATPLLMRPLSMDNMLQAPVKNVTKYGNMTQDHVMH
LLTKSGPVNYPQLKGSFPENLKHLKNSMNGLDWKVFESWMKQWLLFEMSKNSLEEKQPTQTPPK
EPLDMEDPSSGLGVTKQDMGQMFL

hide sequence

RefSeq Acc Id:	XP_006254823 ⟸ XM_006254761
- Peptide Label:	isoform X1
- UniProtKB:	P10247 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MDDQRDLISNHEQLPILGQRARAPESNCNRGVLYTSVSVLVALLLAGQATTAYFLYQQQGRLDK LTVTSQNLQLENLRMKLPKSAKPVSPMRMATPLLMRPLSMDNMLQAPVKNVTKYGNMTQDHVMH LLTKSGPVNYPQLKGSFPENLKHLKNSMNGLDWKVFESWMKQWLLFEMSKNSLEEKQPTQTPPK VLTKCQEEVSHIPDVHPGAFRPKCDENGNYMPLQCHGSTGYCWCVFPNGTEVPHTKSRGRHNCS EPLDMEDPSSGLGVTKQDMGQMFL hide sequence

RefSeq Acc Id:

ENSRNOP00000025342 ⟸ ENSRNOT00000025344

RefSeq Acc Id:

ENSRNOP00000025354 ⟸ ENSRNOT00000025354

Protein Domains

MHC2-interact MHCassoc_trimer Thyroglobulin type-1

Transcriptome

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

Promoters

RGD ID:

13700807

Promoter ID:

EPDNEW_R11331

Type:

multiple initiation site

Name:

Cd74_1

Description:

CD74 molecule

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	18	56,071,495 - 56,071,555	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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)

Visual

CSV

TAB

Printer

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

GH/OmrMcwi (MCW)

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CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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:2313	AgrOrtholog
Ensembl Genes	ENSRNOG00000018735	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000025342	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000025354	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000025344	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000025354	UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.870.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	4.10.800.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:6890709	IMAGE-MGC_LOAD
InterPro	CD74_antigen	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	MHC_II-assoc_invar/CLIP_MHC-bd	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	MHC_II-assoc_invar_chain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	MHC_II-assoc_invariant_trimer	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	MHCII_invariant_trimer_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Thyroglobulin_1	UniProtKB/Swiss-Prot
	Thyroglobulin_1_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:25599	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:72926	IMAGE-MGC_LOAD
NCBI Gene	25599	ENTREZGENE
Pfam	MHC2-interact	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	MHCassoc_trimer	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Thyroglobulin_1	UniProtKB/Swiss-Prot
PhenoGen	Cd74	PhenoGen
PIRSF	CD74_antigen	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS	CD74ANTIGEN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	THYROGLOBULIN_1_1	UniProtKB/Swiss-Prot
	THYROGLOBULIN_1_2	UniProtKB/Swiss-Prot
SMART	SM00211	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF48305	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF57610	UniProtKB/Swiss-Prot
TIGR	TC217441
UniProt	HG2A_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q6GT70	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-01-13	Cd74	CD74 molecule	Cd74	Cd74 molecule, major histocompatibility complex, class II invariant chain	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-29	Cd74	Cd74 molecule, major histocompatibility complex, class II invariant chain	Cd74	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Cd74	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)		CD74 antigen (invariant polpypeptide of major histocompatibility class II antigen-associated)	Name updated	1299863	APPROVED
2002-06-10	Cd74	CD74 antigen (invariant polpypeptide of major histocompatibility class II antigen-associated)			Symbol and Name status set to approved	70586	APPROVED

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

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

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

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

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Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)