LOC100970847 (HLA class II histocompatibility antigen, DO beta chain) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LOC100970847 (HLA class II histocompatibility antigen, DO beta chain) Pan paniscus
Analyze
Symbol: LOC100970847 (Ensembl: HLA-DOB)
Name: HLA class II histocompatibility antigen, DO beta chain (Ensembl:major histocompatibility complex, class II, DO beta)
RGD ID: 11738687
Description: ENCODES a protein that exhibits MHC class II protein complex binding (inferred); INVOLVED IN adaptive immune response (inferred); antigen processing and presentation (inferred); antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (inferred); ASSOCIATED WITH proteasome-associated autoinflammatory syndrome 1 (ortholog); FOUND IN endosome (inferred); endosome membrane (inferred); lysosomal membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2547,287,076 - 47,299,056 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1643,158,633 - 43,171,752 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0632,381,463 - 32,387,377 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1633,497,199 - 33,501,542 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,497,652 - 33,501,451 (-)Ensemblpanpan1.1panPan2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
LOC100970847
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2547,287,076 - 47,299,056 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1643,158,633 - 43,171,752 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0632,381,463 - 32,387,377 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1633,497,199 - 33,501,542 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,497,652 - 33,501,451 (-)Ensemblpanpan1.1panPan2
HLA-DOB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,812,763 - 32,817,002 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl632,812,763 - 32,820,466 (-)EnsemblGRCh38hg38GRCh38
GRCh37632,780,540 - 32,784,779 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,888,518 - 32,892,803 (-)NCBINCBI36Build 36hg18NCBI36
Build 34632,888,526 - 32,892,760NCBI
Celera634,329,595 - 34,333,880 (-)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef632,522,917 - 32,527,179 (-)NCBIHuRef
CHM1_1632,781,544 - 32,785,829 (-)NCBICHM1_1
T2T-CHM13v2.0632,634,117 - 32,638,355 (-)NCBIT2T-CHM13v2.0
H2-Ob
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,457,879 - 34,464,882 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,457,877 - 34,473,388 (+)EnsemblGRCm39 Ensembl
GRCm381734,238,905 - 34,245,908 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,238,903 - 34,254,414 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,375,850 - 34,382,853 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361733,850,628 - 33,854,100 (+)NCBIMGSCv36mm8
Celera1736,980,110 - 36,996,885 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
RT1-DOb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,621,336 - 4,627,537 (-)NCBIGRCr8
mRatBN7.2204,619,418 - 4,625,627 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,619,816 - 4,625,667 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,372,193 - 5,377,744 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,733,934 - 4,739,485 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,217,240 - 5,222,903 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,020,273 - 4,026,398 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,020,317 - 4,026,346 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,099,866 - 6,105,845 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,753,940 - 4,759,648 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,221,090 - 6,226,692 (-)NCBICelera
Cytogenetic Map20p12NCBI
DLA-DOB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,376,957 - 2,384,179 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,378,126 - 2,432,303 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,459,974 - 2,465,584 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0122,652,367 - 2,659,185 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl122,652,372 - 2,699,034 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1122,377,490 - 2,383,108 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0122,458,767 - 2,464,390 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0122,533,116 - 2,538,741 (-)NCBIUU_Cfam_GSD_1.0
LOC101961309
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,022,484 - 38,035,492 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647625,932,968 - 25,936,593 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647625,932,926 - 25,937,024 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLA-DOB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl725,030,444 - 25,037,932 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1725,030,435 - 25,038,196 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2729,242,473 - 29,249,542 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7q1.1NCBI
MHC-DOB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,295,768 - 39,300,032 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1739,295,828 - 39,300,819 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604432,593,845 - 32,598,586 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101702636
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,839,985 - 23,851,756 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475423,846,677 - 23,853,674 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_008960670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JARIFH020000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSPPAT00000031019   ⟹   ENSPPAP00000008383
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl633,497,652 - 33,501,451 (-)Ensembl
RefSeq Acc Id: XM_008960670   ⟹   XP_008958918
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v2547,287,076 - 47,299,056 (-)NCBI
NHGRI_mPanPan1643,158,633 - 43,171,752 (-)NCBI
Mhudiblu_PPA_v0632,381,463 - 32,387,377 (-)NCBI
PanPan1.1633,497,199 - 33,501,542 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008958918 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000008383
  ENSPPAP00000008383.1
Reference Protein Sequences
RefSeq Acc Id: XP_008958918   ⟸   XM_008960670
- UniProtKB: A0A2R8ZZI9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSPPAP00000008383   ⟸   ENSPPAT00000031019
Protein Domains
Ig-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000027428 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000031019.1 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/MHC_CS UniProtKB/TrEMBL
  Ig_C1-set 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 LOC100970847 ENTREZGENE
PANTHER HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DO BETA CHAIN UniProtKB/TrEMBL
  MHC CLASS II-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART IGc1 UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
  SSF54452 UniProtKB/TrEMBL
UniProt A0A2R8ZZI9 ENTREZGENE, UniProtKB/TrEMBL