RT1-Hb-ps1 (RT1 class II, locus Hb, pseudogene 1) - Rat Genome Database

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Gene: RT1-Hb-ps1 (RT1 class II, locus Hb, pseudogene 1) Rattus norvegicus
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Symbol: RT1-Hb-ps1
Name: RT1 class II, locus Hb, pseudogene 1
RGD ID: 1595866
Description: Predicted to enable peptide antigen binding activity. Predicted to be involved in several processes, including T cell receptor signaling pathway; antigen processing and presentation of exogenous peptide antigen via MHC class II; and positive regulation of type II interferon production. Predicted to be located in cell surface. Predicted to be part of MHC class II protein complex; INTERACTS WITH 17beta-estradiol (ortholog); 3-Nitrobenzanthrone (ortholog); amiodarone (ortholog).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: AC098547.2; LOC688544; null; RT1 class II, locus Hb; RT1 class II, locus Hb (mapped); RT1-Hb; RT1-Hb_mapped; similar to HLA class II histocompatibility antigen, DP(W4) beta chain precursor
RGD Orthologs
Human
Chinchilla
Bonobo
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,777,494 - 4,781,486 (+)NCBIGRCr8
mRatBN7.2204,775,598 - 4,779,590 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,774,650 - 4,780,618 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0203,866,361 - 3,870,353 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,866,636 - 3,870,351 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,945,754 - 5,949,746 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,913,121 - 4,917,113 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,376,076 - 6,380,068 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:7721355   PMID:11685465   PMID:15060004  


Genomics

Comparative Map Data
RT1-Hb-ps1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,777,494 - 4,781,486 (+)NCBIGRCr8
mRatBN7.2204,775,598 - 4,779,590 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,774,650 - 4,780,618 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0203,866,361 - 3,870,353 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,866,636 - 3,870,351 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,945,754 - 5,949,746 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,913,121 - 4,917,113 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,376,076 - 6,380,068 (+)NCBICelera
Cytogenetic Map20p12NCBI
HLA-DPB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,075,990 - 33,089,696 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl633,075,936 - 33,089,696 (+)EnsemblGRCh38hg38GRCh38
GRCh37633,043,767 - 33,057,473 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,151,738 - 33,162,954 (+)NCBINCBI36Build 36hg18NCBI36
Build 34633,151,737 - 33,162,954NCBI
Celera634,592,531 - 34,609,302 (+)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef632,786,143 - 32,799,913 (+)NCBIHuRef
CHM1_1633,045,380 - 33,059,156 (+)NCBICHM1_1
T2T-CHM13v2.0632,897,341 - 32,911,047 (+)NCBIT2T-CHM13v2.0
LOC102026469
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,635,538 - 1,669,042 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,655,092 - 1,666,552 (+)NCBIChiLan1.0ChiLan1.0
LOC100995226
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2547,554,419 - 47,565,212 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1643,426,026 - 43,436,864 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0632,648,780 - 32,659,613 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1633,763,566 - 33,774,387 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,763,566 - 33,774,387 (+)Ensemblpanpan1.1panPan2
LOC101963197
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,219,177 - 38,229,467 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647625,730,596 - 25,741,145 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647625,730,800 - 25,741,089 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MHC-DPB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,996,329 - 39,007,097 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604432,914,008 - 32,924,191 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101697345
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,658,339 - 23,672,663 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475423,661,031 - 23,672,549 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RT1-Hb-ps1
142 total Variants

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
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
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
7175096Tcs1T cell selection QTL 1T cell selection trait (VT:0004917)expression2047270785024580Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
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
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
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
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)20460660717617956Rat
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
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
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
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat

Markers in Region
BM385745  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0205,941,946 - 5,942,132NCBIRnor5.0
Rnor_5.0207,362,258 - 7,362,444NCBIRnor5.0
RGSC_v3.4204,920,735 - 4,920,920UniSTSRGSC3.4
Celera206,383,690 - 6,383,875UniSTS
RH 3.4 Map2071.8UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSRNOT00000092266   ⟹   ENSRNOP00000080109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,775,374 - 4,779,314 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092363   ⟹   ENSRNOP00000083233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,775,404 - 4,779,314 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101039   ⟹   ENSRNOP00000079264
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,774,650 - 4,779,665 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101880   ⟹   ENSRNOP00000083914
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,774,757 - 4,779,678 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117027   ⟹   ENSRNOP00000079474
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,774,650 - 4,780,618 (+)Ensembl
Protein Sequences
Ensembl Protein ENSRNOP00000079264.1
  ENSRNOP00000079474.1
  ENSRNOP00000080109.1
  ENSRNOP00000083233.1
  ENSRNOP00000083914.1
Ensembl Acc Id: ENSRNOP00000083914   ⟸   ENSRNOT00000101880
Ensembl Acc Id: ENSRNOP00000080109   ⟸   ENSRNOT00000092266
Ensembl Acc Id: ENSRNOP00000079264   ⟸   ENSRNOT00000101039
Ensembl Acc Id: ENSRNOP00000083233   ⟸   ENSRNOT00000092363
Ensembl Acc Id: ENSRNOP00000079474   ⟸   ENSRNOT00000117027
Protein Domains
Ig-like   Immunoglobulin C1-set   MHC class II beta chain N-terminal

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-4545 BioCyc
Ensembl Genes ENSRNOG00000061936 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000092266.2 UniProtKB/TrEMBL
  ENSRNOT00000092363.2 UniProtKB/TrEMBL
  ENSRNOT00000101039.1 UniProtKB/TrEMBL
  ENSRNOT00000101880.1 UniProtKB/TrEMBL
  ENSRNOT00000117027.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold 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 RT1-Hb-ps1 ENTREZGENE
PANTHER HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DP BETA 1 CHAIN UniProtKB/TrEMBL
  MHC CLASS II-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/TrEMBL
PhenoGen RT1-Hb-ps1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000061936 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
  SSF54452 UniProtKB/TrEMBL
UniProt A0A8I5ZMT3_RAT UniProtKB/TrEMBL
  A0A8I6G527_RAT UniProtKB/TrEMBL
  A0A8I6G660_RAT UniProtKB/TrEMBL
  A0A8I6G8N5_RAT UniProtKB/TrEMBL
  A0A8I6GBA0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-05-27 RT1-Hb-ps1  RT1 class II, locus Hb, pseudogene 1  AC098547.2    Data merged from RGD:15014460 737654 PROVISIONAL
2019-11-08 AC098547.2        Symbol and Name status set to provisional 45752 PROVISIONAL
2012-02-24 RT1-Hb-ps1  RT1 class II, locus Hb, pseudogene 1  RT1-Hb  RT1 class II, locus Hb  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-09-08 RT1-Hb  RT1 class II, locus Hb  LOC688544  similar to HLA class II histocompatibility antigen, DP(W4) beta chain precursor  Data merged from RGD:1587635 737654 APPROVED
2007-04-12 RT1-Hb  RT1 class II, locus Hb  RT1-Hb_mapped  RT1 class II, locus Hb (mapped)  Data merged from RGD:3488 737654 APPROVED
2006-11-20 RT1-Hb  RT1 class II, locus Hb      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 RT1-Hb_mapped  RT1 class II, locus Hb(mapped)  RT1-Hb  RT1 class II, locus Hb  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-19 LOC688544  similar to HLA class II histocompatibility antigen, DP(W4) beta chain precursor      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 RT1-Hb  RT1 class II, locus Hb      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-Hb  RT1 class II, locus Hb      Symbol and Name status set to approved 70586 APPROVED