RT1-CE5 (RT1 class I, locus CE5) - Rat Genome Database
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Gene: RT1-CE5 (RT1 class I, locus CE5) Rattus norvegicus
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Symbol: RT1-CE5
Name: RT1 class I, locus CE5
RGD ID: 1595868
Description: Predicted to have several functions, including 14-3-3 protein binding activity; TAP binding activity; and beta-2-microglobulin binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and regulation of lymphocyte mediated immunity. Predicted to localize to several cellular components, including MHC class Ib protein complex; bounding membrane of organelle; and external side of plasma membrane. Human ortholog(s) of this gene implicated in several diseases, including asthma (multiple); autoimmune disease (multiple); eye disease (multiple); human immunodeficiency virus infectious disease (multiple); and inner ear disease (multiple). Orthologous to several human genes including HLA-F (major histocompatibility complex, class I, F); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC112896; MHC class I protein; MHC class Ib antigen; RT1 class I, CE5; RT1 class I, CE7; RT1-C/E5; RT1-CE7; rt1-E2; rt1-El
RGD Orthologs
Human
Mouse
Dog
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,403,418 - 3,479,476 (-)NCBI
Rnor_6.0 Ensembl204,892,702 - 4,896,991 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0204,892,702 - 4,896,993 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,968,846 - 6,973,135 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,509,593 - 3,513,732NCBIRGSC3.4rn4RGSC3.4
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10605026   PMID:10866120   PMID:11238641   PMID:11491540   PMID:12477932   PMID:12837137   PMID:16709803   PMID:19946888   PMID:20865824   PMID:23851683   PMID:24018270   PMID:26928464  
PMID:27455421   PMID:28636952   PMID:29531166  


Genomics

Comparative Map Data
RT1-CE5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,403,418 - 3,479,476 (-)NCBI
Rnor_6.0 Ensembl204,892,702 - 4,896,991 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0204,892,702 - 4,896,993 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,968,846 - 6,973,135 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,509,593 - 3,513,732NCBIRGSC3.4rn4RGSC3.4
Cytogenetic Map20p12NCBI
HLA-F
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl629,722,775 - 29,738,528 (+)EnsemblGRCh38hg38GRCh38
GRCh38629,723,434 - 29,740,355 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37629,691,211 - 29,695,073 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37629,691,117 - 29,695,073 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36629,799,096 - 29,803,052 (+)NCBINCBI36hg18NCBI36
Build 34629,799,219 - 29,802,262NCBI
Celera631,294,546 - 31,298,502 (+)NCBI
Cytogenetic Map6p22.1NCBI
HuRef629,494,781 - 29,498,733 (+)NCBIHuRef
CHM1_1629,693,239 - 29,697,195 (+)NCBICHM1_1
Gm11127
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391736,366,708 - 36,369,263 (-)NCBIGRCm39mm39
GRCm381736,055,816 - 36,058,371 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1736,055,816 - 36,058,371 (-)EnsemblGRCm38mm10GRCm38
Cytogenetic Map17B1NCBI
cM Map1718.88NCBI
DLA-79
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1841,142,307 - 41,170,100 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11841,142,312 - 41,170,018 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1

Position Markers
D20Wox23  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0206,994,638 - 6,994,850NCBIRnor5.0
Rnor_5.0206,969,406 - 6,969,629NCBIRnor5.0
RGSC_v3.4203,510,154 - 3,510,376UniSTSRGSC3.4
RGSC_v3.4203,536,556 - 3,536,767UniSTSRGSC3.4
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2039105555533640Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2040391135875448Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:386
Count of miRNA genes:227
Interacting mature miRNAs:263
Transcripts:ENSRNOT00000060980
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 8 27 11 19 11 2 1 12 13 11
Low 31 30 30 30 8 9 69 23 28 8
Below cutoff 4 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001033986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098658 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF210328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF210329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ243338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ276126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ314857 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ315490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ537441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MG963102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MG963103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000060980   ⟹   ENSRNOP00000057699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,892,702 - 4,896,991 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,896,031 - 4,896,969 (-)Ensembl
RefSeq Acc Id: NM_001008843   ⟹   NP_001008843
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,475,277 - 3,479,414 (-)NCBI
Rnor_6.0204,892,702 - 4,896,991 (-)NCBI
Rnor_5.0206,968,846 - 6,973,135 (-)NCBI
RGSC_v3.4203,509,593 - 3,513,732 (-)RGD
Celera203,404,618 - 3,422,730 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001033986   ⟹   NP_001029158
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,475,277 - 3,479,414 (-)NCBI
Rnor_6.0204,892,702 - 4,896,991 (-)NCBI
Rnor_5.0206,968,846 - 6,973,135 (-)NCBI
RGSC_v3.4203,509,593 - 3,513,732 (-)RGD
Celera203,404,618 - 3,422,730 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601637   ⟹   XP_017457126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,892,702 - 4,896,993 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098655   ⟹   XP_038954583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,271 - 3,461,977 (-)NCBI
RefSeq Acc Id: XM_039098656   ⟹   XP_038954584
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,271 - 3,461,977 (-)NCBI
RefSeq Acc Id: XM_039098657   ⟹   XP_038954585
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,271 - 3,461,973 (-)NCBI
RefSeq Acc Id: XM_039098658   ⟹   XP_038954586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,403,418 - 3,461,971 (-)NCBI
RefSeq Acc Id: XM_039098659   ⟹   XP_038954587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,457,971 - 3,461,976 (-)NCBI
RefSeq Acc Id: XM_039098660   ⟹   XP_038954588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,457,971 - 3,479,476 (-)NCBI
RefSeq Acc Id: XM_039098661   ⟹   XP_038954589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,617 - 3,437,237 (-)NCBI
RefSeq Acc Id: XM_039098662   ⟹   XP_038954590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,271 - 3,461,975 (-)NCBI
RefSeq Acc Id: XM_039098663   ⟹   XP_038954591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,457,971 - 3,461,976 (-)NCBI
RefSeq Acc Id: XM_039098664   ⟹   XP_038954592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,617 - 3,437,237 (-)NCBI
RefSeq Acc Id: XM_039098665   ⟹   XP_038954593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,403,424 - 3,437,237 (-)NCBI
RefSeq Acc Id: XM_039098666   ⟹   XP_038954594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,457,971 - 3,461,975 (-)NCBI
RefSeq Acc Id: XM_039098667   ⟹   XP_038954595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,475,277 - 3,479,476 (-)NCBI
RefSeq Acc Id: XM_039098669   ⟹   XP_038954597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,617 - 3,437,237 (-)NCBI
RefSeq Acc Id: XM_039098670   ⟹   XP_038954598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,457,971 - 3,461,975 (-)NCBI
RefSeq Acc Id: XM_039098671   ⟹   XP_038954599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,475,277 - 3,479,476 (-)NCBI
RefSeq Acc Id: XM_039098672   ⟹   XP_038954600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,431,509 - 3,437,237 (-)NCBI
RefSeq Acc Id: XM_039098673   ⟹   XP_038954601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,617 - 3,437,237 (-)NCBI
RefSeq Acc Id: XR_005497231
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,417,617 - 3,437,237 (-)NCBI
RefSeq Acc Id: XR_005497232
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,431,509 - 3,437,237 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001008843 (Get FASTA)   NCBI Sequence Viewer  
  NP_001029158 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954583 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954584 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954585 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954586 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954587 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954588 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954589 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954590 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954591 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954592 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954593 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954594 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954595 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954597 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954598 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954599 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954600 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954601 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98841 (Get FASTA)   NCBI Sequence Viewer  
  AVP72132 (Get FASTA)   NCBI Sequence Viewer  
  AVP72133 (Get FASTA)   NCBI Sequence Viewer  
  CAB46085 (Get FASTA)   NCBI Sequence Viewer  
  CAB86228 (Get FASTA)   NCBI Sequence Viewer  
  CAC48028 (Get FASTA)   NCBI Sequence Viewer  
  CAC85699 (Get FASTA)   NCBI Sequence Viewer  
  CAD60939 (Get FASTA)   NCBI Sequence Viewer  
  CAD60940 (Get FASTA)   NCBI Sequence Viewer  
  CAD60941 (Get FASTA)   NCBI Sequence Viewer  
  CAD60942 (Get FASTA)   NCBI Sequence Viewer  
  CAD60943 (Get FASTA)   NCBI Sequence Viewer  
  CAD60944 (Get FASTA)   NCBI Sequence Viewer  
  CAD60946 (Get FASTA)   NCBI Sequence Viewer  
  CAE84011 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001008843   ⟸   NM_001008843
- Peptide Label: isoform 1 precursor
- UniProtKB: Q861J1 (UniProtKB/TrEMBL),   Q861Q0 (UniProtKB/TrEMBL),   Q95II0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001029158   ⟸   NM_001033986
- Peptide Label: isoform 2 precursor
- UniProtKB: Q95II0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457126   ⟸   XM_017601637
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000057699   ⟸   ENSRNOT00000060980
RefSeq Acc Id: XP_038954586   ⟸   XM_039098658
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954593   ⟸   XM_039098665
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038954584   ⟸   XM_039098656
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954583   ⟸   XM_039098655
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954590   ⟸   XM_039098662
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038954585   ⟸   XM_039098657
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954601   ⟸   XM_039098673
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038954597   ⟸   XM_039098669
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038954592   ⟸   XM_039098664
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038954589   ⟸   XM_039098661
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038954600   ⟸   XM_039098672
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038954588   ⟸   XM_039098660
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038954591   ⟸   XM_039098663
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038954587   ⟸   XM_039098659
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038954598   ⟸   XM_039098670
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038954594   ⟸   XM_039098666
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038954599   ⟸   XM_039098671
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038954595   ⟸   XM_039098667
- Peptide Label: isoform X13
Protein Domains
Ig-like

Transcriptome

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

Promoters
RGD ID:13701371
Promoter ID:EPDNEW_R11894
Type:initiation region
Name:RT1-CE5_1
Description:RT1 class I, locus CE5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11896  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,896,966 - 4,897,026EPDNEW
RGD ID:13701376
Promoter ID:EPDNEW_R11895
Type:initiation region
Name:RT1-CE7_2
Description:RT1 class I, locus CE7
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11886  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,896,984 - 4,897,044EPDNEW
RGD ID:13701373
Promoter ID:EPDNEW_R11896
Type:initiation region
Name:RT1-CE5_2
Description:RT1 class I, locus CE5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11894  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,897,018 - 4,897,078EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 6969439 6969440 C A snv DOB/Oda (KyushuU), LE/Stm (KyushuU)
20 6969445 6969446 G A snv DOB/Oda (KyushuU), LE/Stm (KyushuU)
20 6969457 6969458 T A snv F344/Stm (KyushuU), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), F344/Jcl (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU)
20 6969476 6969477 C T snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 6969747 6969748 T A snv F344/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), F344/Jcl (KyushuU), F344/NSlc (KyushuU)
20 6969938 6969939 T G snv NIG-III/Hok (KyushuU)
20 6969971 6969972 C A snv Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), BUF/MNa (KyushuU), ZF (KyushuU), KFRS3B/Kyo (KyushuU), LEC/Tj (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU)
20 6970266 6970267 G A snv LE/OrlBarth (UDEL)
20 6970355 6970356 C T snv Crl:SD (UDEL), GH/OmrMcwi (MCW), SDLEF7/Barth (UDEL), ACI/EurMcwi (MCW), LE/OrlBarth (UDEL)
20 6970359 6970360 T C snv Crl:SD (UDEL), SDLEF7/Barth (UDEL)
20 6970448 6970449 G T snv LE/OrlBarth (UDEL)
20 6971570 6971571 C A snv NIG-III/Hok (KyushuU)
20 6972452 6972453 G T snv F344/Stm (KyushuU)
20 6972512 6972513 C T snv SDLEF7/Barth (UDEL)
20 6972539 6972540 C T snv SS/JrHsdMcwi (MCW)
20 6972542 6972543 G C snv SDLEF7/Barth (UDEL)
20 6972544 6972545 G T snv GH/OmrMcwi (MCW)
20 6972602 6972603 C G snv IS/Kyo (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), IS-Tlk/Kyo (KyushuU)
20 6972632 6972633 C G snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU)
20 6972638 6972639 C T snv BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU)
20 6972671 6972672 G C snv COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW)
20 6973042 6973043 G A snv Crl:SD (UDEL)
20 6973053 6973054 G A snv SDLEF7/Barth (UDEL)
20 6973075 6973076 G C snv SDLEF7/Barth (UDEL)
20 6973081 6973082 G A snv SS/JrHsdMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), ACI/EurMcwi (MCW)
20 6973099 6973100 T C snv SR/JrHsd (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), DOB/Oda (KyushuU), F344/Jcl (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), IS/Kyo (KyushuU), SS/JrHsdMcwi (MCW)
20 6973105 6973106 C T snv ACI/EurMcwi (MCW), F344/NSlc (KyushuU), IS-Tlk/Kyo (KyushuU), LE/Stm (KyushuU), HWY/Slc (KyushuU), F344/DuCrlCrlj (KyushuU), SS/JrHsdMcwi (MCW), F344/Stm (KyushuU), IS/Kyo (KyushuU), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), SR/JrHsd (MCW), F344/Jcl (KyushuU), DOB/Oda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 4893295 4893296 C A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW)
20 4893301 4893302 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW)
20 4893313 4893314 T A snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 4893332 4893333 C T snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), F344/NRrrc (MCW)
20 4893812 4893813 C A snv SHR/NHsd (RGD), GK/Ox (RGD), SHRSP/Gcrc (RGD)
20 4893827 4893828 C A snv FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW)
20 4894109 4894110 T A snv CDR, CDS
20 4894131 4894132 C G snv CDS, CDR
20 4894211 4894212 C T snv GH/OmrMcwi (MCW)
20 4894260 4894261 C G snv SBN/Ygl (MCW), SBH/Ygl (MCW)
20 4896275 4896276 C T snv SR/JrHsd (MCW)
20 4896308 4896309 G T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
20 4896368 4896369 C T snv SBH/Ygl (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), CDS, CDR, SBN/Ygl (MCW)
20 4896395 4896396 C T snv SBH/Ygl (MCW), SHRSP/Gcrc (RGD), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW)
20 4896398 4896399 G C snv CDS, CDR
20 4896400 4896401 G T snv GH/OmrMcwi (MCW), CDR, CDS
20 4896419 4896420 C G snv CDS, CDR
20 4896458 4896459 C G snv SBH/Ygl (MCW), SBN/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)
20 4896488 4896489 C G snv CDR, WN/N (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SBN/Ygl (MCW), CDS, ACI/N (MCW), WKY/N (MCW)
20 4896494 4896495 C G snv CDR
20 4896506 4896507 C T snv SBH/Ygl (MCW), SBN/Ygl (MCW)
20 4896527 4896528 G C snv ACI/EurMcwi (MCW), SBN/Ygl (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 4896898 4896899 G A snv FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBN/Ygl (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), SS/JrHsdMcwi (MCW)
20 4896909 4896910 G A snv SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), CDS, CDR, SR/JrHsd (MCW)
20 4896937 4896938 G A snv GH/OmrMcwi (MCW), SR/JrHsd (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), CDR, CDS
20 4896955 4896956 T C snv SR/JrHsd (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), CDS, GH/OmrMcwi (MCW), SBH/Ygl (MCW), CDR, ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW)
20 4896961 4896962 C T snv SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), CDS, ACI/EurMcwi (MCW), CDR, FHH/EurMcwi (MCW), SR/JrHsd (MCW), COP/CrCrl (MCW & UW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3510192 3510193 G A snv LE/Stm (KNAW)
20 3510204 3510205 T A snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 3510223 3510224 C T snv F344/NRrrc (KNAW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
20 3510477 3510478 C A snv SHRSP/Gcrc (ICL), SHR/OlaIpcv (KNAW), GK/Ox (ICL), SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), SHR/NHsd (ICL), SHR/OlaIpcv (ICL)
20 3510703 3510704 C A snv SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), SHR/OlaIpcv (KNAW)
20 3510718 3510719 C A snv FHL/EurMcwi (MCW)
20 3511013 3511014 G A snv HCR/1Mco (UMich), LCR/1Mco (UMich)
20 3511083 3511084 G T snv ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW)
20 3511096 3511097 T C snv SR/JrHsd (MCW)
20 3511102 3511103 C T snv SBH/Ygl (ICL), MNS/Gib (ICL), MHS/Gib (ICL), LEW/NCrl (ICL), LEW/Crl (ICL), FHL/EurMcwi (ICL), FHH/EurMcwi (ICL), ACI/EurMcwi (ICL), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), BBDP/WorN (ICL), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich)
20 3511106 3511107 T C snv SR/JrHsd (MCW)
20 3511205 3511206 C T snv HCR/1Mco (UMich), LCR/2Mco (UMich)
20 3513291 3513292 G T snv GH/OmrMcwi (MCW)
20 3513379 3513380 C G snv ACI/N (KNAW), WKY/N (KNAW), WN/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich)
20 3513396 3513397 A G snv LCR/1Mco (UMich), HCR/1Mco (UMich), LCR/2Mco (UMich)
20 3513400 3513401 C A snv LCR/2Mco (UMich)
20 3513418 3513419 G C snv COP/CrCrl (MCW & UW)
20 3513678 3513679 G A snv ACI/EurMcwi (MCW), SR/JrHsd (MCW)
20 3513696 3513697 T C snv COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SR/JrHsd (MCW)
20 3513702 3513703 C T snv COP/CrCrl (MCW & UW), SR/JrHsd (MCW), ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595868 AgrOrtholog
Ensembl Genes ENSRNOG00000000723 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057699 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060980 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7379095 IMAGE-MGC_LOAD
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/TrEMBL
  MHC_I-like_Ag-recog UniProtKB/TrEMBL
  MHC_I-like_Ag-recog_sf UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  MHC_I_a_a1/a2 UniProtKB/TrEMBL
  MHC_I_a_C UniProtKB/TrEMBL
KEGG Report rno:309607 UniProtKB/TrEMBL
MGC_CLONE MGC:112896 IMAGE-MGC_LOAD
NCBI Gene 309607 ENTREZGENE
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-CE5 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt Q861J1 ENTREZGENE, UniProtKB/TrEMBL
  Q861Q0 ENTREZGENE, UniProtKB/TrEMBL
  Q95II0 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F7FP91 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-CE5  RT1 class I, locus CE5  RT1-CE5  RT1 class I, CE5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 RT1-CE5  RT1 class I, CE5      Symbol and Name status set to provisional 70820 PROVISIONAL