Cd74 (CD74 molecule) - Rat Genome Database

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Gene: Cd74 (CD74 molecule) Rattus norvegicus
Analyze
Symbol: Cd74
Name: CD74 molecule
RGD ID: 2313
Description: Predicted to enable several functions, including amyloid-beta binding activity; macrophage migration inhibitory factor binding activity; and signaling receptor binding activity. Predicted to contribute to cytokine binding activity. Involved in cell population proliferation and positive regulation of MAPK cascade. Predicted to be located in several cellular components, including Golgi apparatus; external side of plasma membrane; and multivesicular body. Predicted to be integral component of membrane. Predicted to be part of MHC class II protein complex; NOS2-CD74 complex; and macrophage migration inhibitory factor receptor complex. Predicted to be active in cell surface and cytoplasm. 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21854,256,757 - 54,266,003 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1854,256,778 - 54,266,003 (+)Ensembl
Rnor_6.01856,071,420 - 56,080,851 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1856,071,478 - 56,080,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01855,305,827 - 55,315,246 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41856,756,511 - 56,765,711 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11856,828,786 - 56,837,940 (+)NCBI
Celera1852,411,586 - 52,420,786 (+)NCBICelera
RH 3.4 Map18525.0RGD
Cytogenetic Map18q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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 acetate  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (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)
cadmium dichloride  (EXP)
captan  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
chlordecone  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
clothianidin  (ISO)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
Cuprizon  (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)
ivermectin  (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)
paraquat  (EXP)
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)
temozolomide  (ISO)
testosterone  (EXP,ISO)
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
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  (IDA,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)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21854,256,757 - 54,266,003 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1854,256,778 - 54,266,003 (+)Ensembl
Rnor_6.01856,071,420 - 56,080,851 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1856,071,478 - 56,080,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01855,305,827 - 55,315,246 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41856,756,511 - 56,765,711 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11856,828,786 - 56,837,940 (+)NCBI
Celera1852,411,586 - 52,420,786 (+)NCBICelera
RH 3.4 Map18525.0RGD
Cytogenetic Map18q12.1NCBI
CD74
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5150,400,041 - 150,412,969 (-)EnsemblGRCh38hg38GRCh38
GRCh385150,401,637 - 150,412,910 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375149,779,604 - 149,792,499 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365149,761,393 - 149,772,525 (-)NCBINCBI36hg18NCBI36
Build 345149,761,396 - 149,772,511NCBI
Celera5145,862,277 - 145,873,409 (-)NCBI
Cytogenetic Map5q33.1NCBI
HuRef5144,928,781 - 144,940,080 (-)NCBIHuRef
CHM1_15149,213,619 - 149,224,915 (-)NCBICHM1_1
Cd74
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391860,936,921 - 60,945,724 (+)NCBIGRCm39mm39
GRCm39 Ensembl1860,936,920 - 60,945,724 (+)Ensembl
GRCm381860,803,849 - 60,812,652 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1860,803,848 - 60,812,652 (+)EnsemblGRCm38mm10GRCm38
MGSCv371860,963,503 - 60,972,306 (+)NCBIGRCm37mm9NCBIm37
MGSCv361860,929,247 - 60,938,021 (+)NCBImm8
Celera1862,088,874 - 62,098,436 (+)NCBICelera
Cytogenetic Map18E1NCBI
cM Map1834.41NCBI
Cd74
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554154,129,254 - 4,137,826 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554154,129,151 - 4,138,336 (+)NCBIChiLan1.0ChiLan1.0
CD74
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15151,830,311 - 151,841,334 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5151,830,311 - 151,841,334 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05145,825,635 - 145,836,916 (-)NCBIMhudiblu_PPA_v0panPan3
CD74
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1458,689,745 - 58,698,421 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl458,689,752 - 58,698,151 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha458,456,154 - 58,464,833 (+)NCBI
ROS_Cfam_1.0459,170,613 - 59,179,292 (+)NCBI
UMICH_Zoey_3.1458,959,149 - 58,967,827 (+)NCBI
UNSW_CanFamBas_1.0459,073,563 - 59,082,236 (+)NCBI
UU_Cfam_GSD_1.0459,604,607 - 59,613,287 (+)NCBI
Cd74
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213142,948,591 - 142,958,314 (+)NCBI
SpeTri2.0NW_0049365044,522,576 - 4,532,289 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD74
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12151,402,210 - 151,409,924 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CD74
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12353,008,802 - 53,022,953 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2353,009,394 - 53,022,923 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603424,695,767 - 24,707,325 (+)NCBIVero_WHO_p1.0
Cd74
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247749,699,876 - 9,708,871 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94596  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21854,265,807 - 54,265,953 (+)MAPPERmRatBN7.2
Rnor_6.01856,080,656 - 56,080,801NCBIRnor6.0
Rnor_5.01855,315,051 - 55,315,196UniSTSRnor5.0
RGSC_v3.41856,765,516 - 56,765,661UniSTSRGSC3.4
Celera1852,420,591 - 52,420,736UniSTS
RH 3.4 Map18525.0UniSTS
Cytogenetic Map18q12.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)182896485373964853Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
9589816Gluco68Glucose level QTL 687.250.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)182979296574792965Rat
8694378Bw157Body weight QTL 1573.590.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)182979296574792965Rat
9590318Scort22Serum corticosterone level QTL 227.640.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)182979296574792965Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182979296574792965Rat
738005Anxrr11Anxiety related response QTL 113.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)183003981375039813Rat
61383Bp47Blood pressure QTL 4717.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)183127168160377755Rat
1331742Bp228Blood pressure QTL 2283.88752arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183135940859796643Rat
1331774Bp226Blood pressure QTL 2264.41065arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183135940859796643Rat
1331776Bp225Blood pressure QTL 2252.829arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)183135940859796643Rat
1331798Bp224Blood pressure QTL 2243.53873arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183135940859796643Rat
1331727Bp237Blood pressure QTL 2373.053arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183135940861698465Rat
61429Cia17Collagen induced arthritis QTL 174.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)183135940870263868Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183135940883218561Rat
6903347Bp350Blood pressure QTL 3504.4arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183135953059796478Rat
631274Sprol1Serum protein level QTL 15.3blood total protein amount (VT:0005567)serum total protein level (CMO:0000661)183139332077209694Rat
631518Bw11Body weight QTL 112.8body mass (VT:0001259)body weight (CMO:0000012)183587072380870723Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)183819245583192455Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184143297183828827Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184334502283828827Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184664067583828827Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184664067583828827Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184664067583828827Rat
1331806Bp229Blood pressure QTL 2294.36484arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184671876357867167Rat
1331736Bp227Blood pressure QTL 2272.791arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)184671876359796643Rat
1331780Bp238Blood pressure QTL 2383.269arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184671876359796643Rat
6903345Bp349Blood pressure QTL 3493.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184671893559796478Rat
6903349Bp351Blood pressure QTL 3513.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184671893559796478Rat
6903351Bp352Blood pressure QTL 3523.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184671893559796478Rat
61360EaeyExperimental allergic encephalomyelitis QTL y3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)184698893960377753Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)184852004483828827Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)184852004483828827Rat
7411719Strs5Sensitivity to stroke QTL 59.4cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)184999995865845095Rat
2293658Bmd23Bone mineral density QTL 237.30.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)185146473363636873Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185146473383218561Rat
1331730Scl27Serum cholesterol level QTL 273.826blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)185229287559796643Rat
1331752Bw27Body weight QTL 272.963body mass (VT:0001259)body weight (CMO:0000012)185229287565845095Rat
1359020Ppulsi2Prepulse inhibition QTL 22.71prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)185229287573997283Rat
1600375Mcs22Mammary carcinoma susceptibility QTL 223.3mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)185253976363933058Rat
631509Sald2Serum aldosterone level QTL 22.9blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)185253976369140759Rat
12880368Bw187Body weight QTL 1870.045body mass (VT:0001259)body weight (CMO:0000012)185253976376104388Rat
12904067Cm122Cardiac mass QTL 1220.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)185253976376104388Rat
12904069Cm123Cardiac mass QTL 1230.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)185253976376104388Rat
12904070Cm124Cardiac mass QTL 1240.01heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)185253976376104388Rat
12904071Am18Aortic mass QTL 180.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)185253976376104388Rat
12904073Kidm71Kidney mass QTL 710.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)185253976376104388Rat
2301417Bp319Blood pressure QTL 3190.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185253976376104388Rat
1300125Rf26Renal function QTL 263.2urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)185253986365844950Rat

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

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 AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1854,256,820 - 54,265,999 (+)Ensembl
Rnor_6.0 Ensembl1856,071,478 - 56,080,849 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000025354   ⟹   ENSRNOP00000025354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1854,256,778 - 54,266,003 (+)Ensembl
Rnor_6.0 Ensembl1856,071,574 - 56,080,397 (+)Ensembl
RefSeq Acc Id: NM_013069   ⟹   NP_037201
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21854,256,803 - 54,266,003 (+)NCBI
Rnor_6.01856,071,478 - 56,080,851 (+)NCBI
Rnor_5.01855,305,827 - 55,315,246 (+)NCBI
RGSC_v3.41856,756,511 - 56,765,711 (+)RGD
Celera1852,411,586 - 52,420,786 (+)RGD
Sequence:
RefSeq Acc Id: XM_006254761   ⟹   XP_006254823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21854,256,757 - 54,266,003 (+)NCBI
Rnor_6.01856,071,420 - 56,080,851 (+)NCBI
Rnor_5.01855,305,827 - 55,315,246 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037201   ⟸   NM_013069
- UniProtKB: P10247 (UniProtKB/Swiss-Prot),   Q6GT70 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254823   ⟸   XM_006254761
- Peptide Label: isoform X1
- UniProtKB: P10247 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025342   ⟸   ENSRNOT00000025344
RefSeq Acc Id: ENSRNOP00000025354   ⟸   ENSRNOT00000025354
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 AssemblyChrPosition (strand)Source
Rnor_6.01856,071,495 - 56,071,555EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2313 AgrOrtholog
Ensembl Genes ENSRNOG00000018735 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000025342 UniProtKB/Swiss-Prot
  ENSRNOP00000025354 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025344 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