RT1-Db2 (RT1 class II, locus Db2) - Rat Genome Database

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Gene: RT1-Db2 (RT1 class II, locus Db2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-Db2
Name: RT1 class II, locus Db2
RGD ID: 1595922
Description: Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Predicted to be involved in several processes, including antigen processing and presentation of exogenous peptide antigen via MHC class II; peptide antigen assembly with MHC class II protein complex; and positive regulation of T cell activation. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Human ortholog(s) of this gene implicated in several diseases, including asthma (multiple); autoimmune disease (multiple); bacterial infectious disease (multiple); eye disease (multiple); and sarcoidosis (multiple). Orthologous to several human genes including HLA-DRB1 (major histocompatibility complex, class II, DR beta 1); HLA-DRB3 (major histocompatibility complex, class II, DR beta 3); and HLA-DRB4 (major histocompatibility complex, class II, DR beta 4); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Db2; MHC class II beta chain; RT1 class II, locus Db2 (mapped); RT1-Db2_mapped
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,521,929 - 4,541,654 (-)NCBIGRCr8
mRatBN7.2204,520,723 - 4,539,724 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,520,713 - 4,539,705 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,283,588 - 5,301,560 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,645,329 - 4,663,301 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,118,426 - 5,137,437 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,106,136 - 4,126,103 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,106,189 - 4,125,387 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,186,186 - 6,216,870 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,643,873 - 4,662,490 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,123,209 - 6,141,825 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1300424   PMID:12136338   PMID:24586191   PMID:26740108  


Genomics

Variants

.
Variants in RT1-Db2
465 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:66
Count of miRNA genes:56
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000042571
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
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
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7175099Tcs2T cell selection QTL 2T cell selection trait (VT:0004917)expression2045040024693102Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
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
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
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
737973Pia21Pristane induced arthritis QTL 214.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2036216564606812Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat

Markers in Region
D20Yum73  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,522,465 - 4,522,797 (-)MAPPERmRatBN7.2
mRatBN7.2204,522,465 - 4,522,579 (-)MAPPERmRatBN7.2
Rnor_6.0204,123,275 - 4,123,635NCBIRnor6.0
Rnor_6.0204,123,522 - 4,123,635NCBIRnor6.0
Rnor_5.0206,203,660 - 6,203,773UniSTSRnor5.0
Rnor_5.0206,203,413 - 6,203,773UniSTSRnor5.0
RGSC_v3.4204,645,291 - 4,645,404UniSTSRGSC3.4
Celera206,124,627 - 6,124,740UniSTS
Cytogenetic Map20 RGD


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 10 37 53 67 66 35 25 35 6 181 84 33 45 49 31

Sequence


Ensembl Acc Id: ENSRNOT00000042571   ⟹   ENSRNOP00000042899
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,523,789 - 4,539,704 (-)Ensembl
Rnor_6.0 Ensembl204,106,189 - 4,124,780 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083085   ⟹   ENSRNOP00000071225
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,520,713 - 4,539,705 (-)Ensembl
Rnor_6.0 Ensembl204,118,461 - 4,125,387 (+)Ensembl
RefSeq Acc Id: NM_001164826   ⟹   NP_001158298
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,522,978 - 4,541,595 (-)NCBI
mRatBN7.2204,521,048 - 4,539,667 (-)NCBI
Rnor_6.0204,106,189 - 4,125,053 (+)NCBI
Rnor_5.0206,186,186 - 6,216,870 (+)NCBI
RGSC_v3.4204,643,873 - 4,662,490 (-)RGD
Celera206,123,209 - 6,141,825 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255911   ⟹   XP_006255973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,521,929 - 4,541,654 (-)NCBI
mRatBN7.2204,520,723 - 4,539,724 (-)NCBI
Rnor_6.0204,106,136 - 4,126,103 (+)NCBI
Rnor_5.0206,186,186 - 6,216,870 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098428   ⟹   XP_038954356
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,521,929 - 4,541,652 (-)NCBI
mRatBN7.2204,520,723 - 4,539,723 (-)NCBI
RefSeq Acc Id: NP_001158298   ⟸   NM_001164826
- Peptide Label: precursor
- UniProtKB: A0A023IKG1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255973   ⟸   XM_006255911
- Peptide Label: isoform X1
- UniProtKB: A0A023IKK2 (UniProtKB/TrEMBL),   D3ZT06 (UniProtKB/TrEMBL),   A0A0G2JZX8 (UniProtKB/TrEMBL),   A0A023IKG1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071225   ⟸   ENSRNOT00000083085
Ensembl Acc Id: ENSRNOP00000042899   ⟸   ENSRNOT00000042571
RefSeq Acc Id: XP_038954356   ⟸   XM_039098428
- Peptide Label: isoform X2
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A023IKK2-F1-model_v2 AlphaFold A0A023IKK2 1-287 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595922 AgrOrtholog
BioCyc Gene G2FUF-4565 BioCyc
Ensembl Genes ENSRNOG00000030431 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042571.6 UniProtKB/TrEMBL
  ENSRNOT00000083085.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 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/Immunoglobulin UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  MHC_II_a/b_N UniProtKB/TrEMBL
  MHC_II_b_N UniProtKB/TrEMBL
NCBI Gene 24981 ENTREZGENE
PANTHER HISTOCOMPATIBILITY 2, CLASS II ANTIGEN E BETA2 UniProtKB/TrEMBL
  MHC CLASS II-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/TrEMBL
PhenoGen RT1-Db2 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030431 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A023IKG1 ENTREZGENE, UniProtKB/TrEMBL
  A0A023IKK2 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JZX8 ENTREZGENE
  A0A0R7FDM2_RAT UniProtKB/TrEMBL
  A0A0R7FDM5_RAT UniProtKB/TrEMBL
  A0A0R7FDM6_RAT UniProtKB/TrEMBL
  A0A8J8YBX6_RAT UniProtKB/TrEMBL
  D3ZT06 ENTREZGENE
UniProt Secondary A0A0G2JZX8 UniProtKB/TrEMBL
  D3ZT06 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-12 RT1-Db2  RT1 class II, locus Db2  RT1-Db2_mapped  RT1 class II, locus Db2 (mapped)  Data merged from RGD:3481 737654 APPROVED
2006-11-20 RT1-Db2_mapped  RT1 class II, locus Db2(mapped)  RT1-Db2  RT1 class II, locus Db2  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-20 RT1-Db2  RT1 class II, locus Db2      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 RT1-Db2  RT1 class II, locus Db2      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-Db2  RT1 class II, locus Db2      Symbol and Name status set to approved 70586 APPROVED