RT1-M3-1 (RT1 class Ib, locus M3, gene 1) - Rat Genome Database

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Gene: RT1-M3-1 (RT1 class Ib, locus M3, gene 1) Rattus norvegicus
Analyze
Symbol: RT1-M3-1
Name: RT1 class Ib, locus M3, gene 1
RGD ID: 3494
Description: Predicted to enable CD8 receptor binding activity; peptide antigen binding activity; and protein homodimerization activity. Predicted to be involved in several processes, including positive regulation of cytokine production; regulation of leukocyte differentiation; and regulation of lymphocyte mediated immunity. Predicted to be located in cis-Golgi network membrane; early endosome; and plasma membrane. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including Stevens-Johnson syndrome; asthma (multiple); autoimmune disease (multiple); eye disease (multiple); and inner ear disease (multiple). Orthologous to several human genes including HLA-B (major histocompatibility complex, class I, B); HLA-C (major histocompatibility complex, class I, C); and HLA-E (major histocompatibility complex, class I, E); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 4B2/3.7; H2-M3; histocompatibility 2, M region locus 3; MHC class I antigen; MHC class I-b antigen M3; RanoM3; RanoM301; RanoM302; RT1 class Ib gene; RT1 class Ib gene, locus M3; RT1 class Ib, locus M3; RT1 class Ib, locus M3-1; RT1-M3
RGD Orthologs
Human
Pig
Alliance Genes
More Info more info ...
Related Pseudogenes: RT1-M3-2-ps   RT1-M3-3-ps  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2201,323,976 - 1,328,126 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl201,287,521 - 1,328,117 (-)Ensembl
Rnor_6.0201,814,661 - 1,833,033 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl201,814,661 - 1,818,800 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0203,856,748 - 3,860,887 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4201,412,553 - 1,416,692 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1201,412,554 - 1,416,692 (-)NCBI
Celera202,034,641 - 2,038,780 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bifenthrin  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bumetanide  (ISO)
cadmium dichloride  (EXP)
carbamazepine  (ISO)
cefadroxil  (ISO)
cefazolin  (ISO)
ciprofloxacin  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
erythromycin A  (ISO)
fulvestrant  (ISO)
furan  (EXP)
glimepiride  (ISO)
ifosfamide  (ISO)
indole-3-methanol  (EXP)
isotretinoin  (ISO)
ketorolac  (ISO)
lisinopril dihydrate  (ISO)
meropenem  (ISO)
methotrexate  (ISO)
mifepristone  (ISO)
Muraglitazar  (EXP)
N-nitrosodimethylamine  (EXP)
omeprazole  (ISO)
paracetamol  (EXP)
phenylmercury acetate  (ISO)
piroxicam  (ISO)
progesterone  (ISO)
pyrimethamine  (ISO)
rifampicin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenate  (ISO)
sodium hydroxide  (ISO)
sulfamethoxazole  (ISO)
sulforaphane  (ISO)
tamibarotene  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP)
valproic acid  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Induction of cell surface human leukocyte antigen-G expression in pandemic H1N1 2009 and seasonal H1N1 influenza virus-infected patients. Chen HX, etal., Hum Immunol. 2011 Feb;72(2):159-65. Epub 2010 Nov 16.
2. Soluble serum HLA-G in children with allergic rhinitis and asthma. Ciprandi G, etal., J Biol Regul Homeost Agents. 2010 Apr-Jun;24(2):221-4.
3. HLA-G polymorphism influences the susceptibility to HCV infection in sickle cell disease patients. Cordero EA, etal., Tissue Antigens. 2009 Oct;74(4):308-13.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. A novel approach to analyze gene expression data demonstrates that the DeltaF508 mutation in CFTR downregulates the antigen presentation pathway. Hampton TH and Stanton BA, Am J Physiol Lung Cell Mol Physiol. 2010 Apr;298(4):L473-82. Epub 2009 Dec 31.
6. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Fine mapping and positional candidate studies identify HLA-G as an asthma susceptibility gene on chromosome 6p21. Nicolae D, etal., Am J Hum Genet. 2005 Feb;76(2):349-57. Epub 2004 Dec 20.
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
12. GOA pipeline RGD automated data pipeline
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Rat RT1 orthologs of mouse H2-M class Ib genes. Wang CR, etal., Immunogenetics 1995;42(1):63-7.
15. Adhesion molecule expression on epithelial cells infected with respiratory syncytial virus. Wang SZ, etal., Eur Respir J. 2000 Feb;15(2):358-66.
16. The HLA-G 14 bp insertion/deletion polymorphism is a putative susceptible factor for active human cytomegalovirus infection in children. Zheng XQ, etal., Tissue Antigens. 2009 Oct;74(4):317-21. Epub 2009 Jul 17.
Additional References at PubMed
PMID:7584149   PMID:10190900   PMID:11290782   PMID:12582157   PMID:12847252   PMID:12853576   PMID:12874224   PMID:16366734   PMID:16455647   PMID:16809620   PMID:18550825   PMID:19304799  
PMID:20448110   PMID:20702625   PMID:22802125   PMID:23184984   PMID:24453251   PMID:28348268  


Genomics

Comparative Map Data
RT1-M3-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2201,323,976 - 1,328,126 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl201,287,521 - 1,328,117 (-)Ensembl
Rnor_6.0201,814,661 - 1,833,033 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl201,814,661 - 1,818,800 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0203,856,748 - 3,860,887 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4201,412,553 - 1,416,692 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1201,412,554 - 1,416,692 (-)NCBI
Celera202,034,641 - 2,038,780 (-)NCBICelera
Cytogenetic Map20p12NCBI
HLA-G
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38629,826,474 - 29,831,021 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl629,826,967 - 29,831,125 (+)EnsemblGRCh38hg38GRCh38
GRCh37629,794,251 - 29,798,798 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36629,903,497 - 29,906,859 (+)NCBINCBI36hg18NCBI36
Build 34629,903,496 - 29,906,859NCBI
Celera631,397,875 - 31,402,019 (+)NCBI
Cytogenetic Map6p22.1NCBI
HuRef629,598,096 - 29,602,239 (+)NCBIHuRef
CHM1_1629,796,551 - 29,800,708 (+)NCBICHM1_1
T2T-CHM13v2.0629,698,275 - 29,702,836 (+)NCBI
SLA-8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1723,622,352 - 23,625,818 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,626,978 - 27,630,425 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7p1.1NCBI


QTLs in Region (mRatBN7.2)
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)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:212
Count of miRNA genes:161
Interacting mature miRNAs:172
Transcripts:ENSRNOT00000000990
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 2 16 19 12 1 20 11
Low 1 43 41 41 41 8 11 62 34 20 8
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_022921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772688 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC112568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF074610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ249342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY263608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U16025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000990   ⟹   ENSRNOP00000000990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,323,978 - 1,328,117 (-)Ensembl
Rnor_6.0 Ensembl201,814,661 - 1,818,800 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000040634   ⟹   ENSRNOP00000046444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,324,547 - 1,328,117 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075244   ⟹   ENSRNOP00000065658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,325,083 - 1,328,117 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl201,814,662 - 1,815,264 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl201,814,889 - 1,815,476 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102823   ⟹   ENSRNOP00000080762
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,323,963 - 1,328,117 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106320   ⟹   ENSRNOP00000079604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,287,521 - 1,328,117 (-)Ensembl
RefSeq Acc Id: NM_022921   ⟹   NP_075210
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2201,323,978 - 1,328,117 (-)NCBI
Rnor_6.0201,814,661 - 1,818,800 (-)NCBI
Rnor_5.0203,856,748 - 3,860,887 (-)NCBI
RGSC_v3.4201,412,553 - 1,416,692 (-)RGD
Celera202,034,641 - 2,038,780 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772688   ⟹   XP_008770910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2201,323,976 - 1,328,126 (-)NCBI
Rnor_6.0201,816,061 - 1,818,811 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_075210   ⟸   NM_022921
- Peptide Label: precursor
- UniProtKB: G3V627 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770910   ⟸   XM_008772688
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000000990   ⟸   ENSRNOT00000000990
RefSeq Acc Id: ENSRNOP00000080762   ⟸   ENSRNOT00000102823
RefSeq Acc Id: ENSRNOP00000065658   ⟸   ENSRNOT00000075244
RefSeq Acc Id: ENSRNOP00000079604   ⟸   ENSRNOT00000106320
RefSeq Acc Id: ENSRNOP00000046444   ⟸   ENSRNOT00000040634
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V627-F1-model_v2 AlphaFold G3V627 1-339 view protein structure

Transcriptome

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

Promoters
RGD ID:13701265
Promoter ID:EPDNEW_R11789
Type:multiple initiation site
Name:RT1-M3-1_1
Description:RT1 class Ib, locus M3, gene 1
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_6.0201,818,795 - 1,818,855EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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
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)
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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)
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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)
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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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)
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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)
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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)
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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)
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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)
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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)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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)
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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 1816763 1816764 T G snv WKY/N (MCW), MR/N (MCW), M520/N (MCW), Buf/N (MCW), WN/N (MCW)
20 1818766 1818767 G A snv SBN/Ygl (RGD), WAG/RijCrl (2020), SBH/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), SBN/Ygl (MCW), SBH/Ygl (MCW), WAG/Rij (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3494 AgrOrtholog
BioCyc Gene G2FUF-5003 BioCyc
Ensembl Genes ENSRNOG00000000763 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000990 ENTREZGENE
  ENSRNOP00000000990.4 UniProtKB/TrEMBL
  ENSRNOP00000046444 ENTREZGENE
  ENSRNOP00000046444.5 UniProtKB/TrEMBL
  ENSRNOP00000065658.3 UniProtKB/TrEMBL
  ENSRNOP00000079604.1 UniProtKB/TrEMBL
  ENSRNOP00000080762.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000990 ENTREZGENE
  ENSRNOT00000000990.6 UniProtKB/TrEMBL
  ENSRNOT00000040634 ENTREZGENE
  ENSRNOT00000040634.6 UniProtKB/TrEMBL
  ENSRNOT00000075244.4 UniProtKB/TrEMBL
  ENSRNOT00000102823.1 UniProtKB/TrEMBL
  ENSRNOT00000106320.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
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:24747 UniProtKB/TrEMBL
NCBI Gene 24747 ENTREZGENE
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PharmGKB HLA-G RGD
PhenoGen RT1-M3-1 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 A0A8I5ZNC4_RAT UniProtKB/TrEMBL
  A0A8I5ZTS2_RAT UniProtKB/TrEMBL
  G3V627 ENTREZGENE, UniProtKB/TrEMBL
  M0R866_RAT UniProtKB/TrEMBL
  Q6MFW8_RAT UniProtKB/TrEMBL
UniProt Secondary F7F5U0 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-12-07 RT1-M3-1  RT1 class Ib, locus M3, gene 1  RT1-M3  RT1 class Ib, locus M3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-09-11 RT1-M3  RT1 class Ib, locus M3  H2-M3  histocompatibility 2, M region locus 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 H2-M3  histocompatibility 2, M region locus 3  RT1-M3  RT1 class Ib, locus M3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 RT1-2.5  RT1 class Ib, locus M3  RT1-M3  RT1 class Ib gene, locus M3  Name updated 625702 APPROVED
2002-06-10 RT1-M3  RT1 class Ib gene, locus M3      Symbol and Name status set to approved 70586 APPROVED