HLA-U (major histocompatibility complex, class I, U (pseudogene)) - 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: HLA-U (major histocompatibility complex, class I, U (pseudogene)) Homo sapiens
Analyze
Symbol: HLA-U
Name: major histocompatibility complex, class I, U (pseudogene)
RGD ID: 1351895
HGNC Page HGNC:23477
Description: INTERACTS WITH aristolochic acid A
Type: pseudo (Ensembl: unprocessed_pseudogene)
RefSeq Status: INFERRED
Previously known as: HLA-21
Related Functional Gene: HLA-A  
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38629,933,764 - 29,934,880 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl629,934,101 - 29,934,286 (+)EnsemblGRCh38hg38GRCh38
GRCh37629,901,541 - 29,902,657 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,009,519 - 30,010,635 (+)NCBINCBI36Build 36hg18NCBI36
Celera631,499,707 - 31,500,823 (+)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef629,699,535 - 29,700,656 (+)NCBIHuRef
CHM1_1629,901,675 - 29,902,795 (+)NCBICHM1_1
T2T-CHM13v2.0629,797,867 - 29,798,946 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:1517563   PMID:10557312  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:304
Count of miRNA genes:277
Interacting mature miRNAs:291
Transcripts:ENST00000418981
Prediction methods: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.

Markers in Region
D6S2033  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37629,842,613 - 29,842,775UniSTSGRCh37
GRCh37629,902,969 - 29,903,130UniSTSGRCh37
Build 36629,950,592 - 29,950,754RGDNCBI36
Celera631,446,412 - 31,446,574RGD
Celera631,501,135 - 31,501,296UniSTS
Cytogenetic Map6p21.3UniSTS
HuRef629,648,093 - 29,648,255UniSTS
HuRef629,700,968 - 29,701,128UniSTS
Stanford-G3 RH Map61490.0UniSTS
NCBI RH Map6495.3UniSTS
GeneMap99-G3 RH Map61622.0UniSTS
RH46786  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37629,902,969 - 29,903,122UniSTSGRCh37
GRCh37629,842,613 - 29,842,767UniSTSGRCh37
Build 36629,950,592 - 29,950,746RGDNCBI36
Celera631,446,412 - 31,446,566RGD
Celera631,501,135 - 31,501,288UniSTS
Cytogenetic Map6p21.3UniSTS
HuRef629,648,093 - 29,648,247UniSTS
HuRef629,700,968 - 29,701,120UniSTS
GeneMap99-GB4 RH Map6119.27UniSTS


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 sensory system adipose tissue appendage
High 1 1 1
Medium 697 1266 480 76 900 32 1368 415 608 69 393 695 44 517 827
Low 1597 1596 1047 384 653 272 2570 1444 2564 219 868 736 122 678 1732
Below cutoff 47 107 68 48 50 48 224 256 395 47 43 57 1 7 189

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000418981
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl629,934,101 - 29,934,286 (+)Ensembl

Additional Information

Database Acc Id Source(s)
COSMIC HLA-U COSMIC
Ensembl Genes ENSG00000228078 Ensembl
GTEx ENSG00000228078 GTEx
HGNC ID HGNC:23477 ENTREZGENE
Human Proteome Map HLA-U Human Proteome Map
NCBI Gene 352965 ENTREZGENE
PharmGKB PA134981635 PharmGKB