Human Gene HLA-DQA2 (ENST00000374940.4_4) from GENCODE V47lift37
  Description: major histocompatibility complex, class II, DQ alpha 2 (from RefSeq NM_020056.5)
Gencode Transcript: ENST00000374940.4_4
Gencode Gene: ENSG00000237541.4_7
Transcript (Including UTRs)
   Position: hg19 chr6:32,709,168-32,714,975 Size: 5,808 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr6:32,709,221-32,714,171 Size: 4,951 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:32,709,168-32,714,975)mRNA (may differ from genome)Protein (255 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HLA-DQA2
Diseases sorted by gene-association score: narcolepsy (2), autoimmune disease of gastrointestinal tract (1), diabetes mellitus, insulin-dependent (1)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 44.88 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 102.92 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.9053-0.262 Picture PostScript Text
3' UTR -125.50637-0.197 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Descriptions from all associated GenBank mRNAs
  L34094 - Human (clone 41) MHC class II HLA-DQA1*0601 mRNA, partial cds.
M95727 - H.sapiens MHC class II HLA-DQA2 mRNA, exon 2.
M95728 - H.sapiens MHC class II HLA-DQA2 mRNA, exon 2.
AF012768 - Homo sapiens MHC class II antigen DQ-A1 chain (allele A1*05011) mRNA, partial cds.
L34088 - Human (clones 5, 9) MHC class II HLA-DQA1*03011 mRNA, partial cds.
L34089 - Human (clones DKB-82, YT-71) MHC class II HLA-DQA1*0302 mRNA, partial cds.
L34352 - Human (clones WL-3 and WL-8) leucocyte antigen DQA1 allele (HLA DQA1-0302) mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000374940.1, ENST00000374940.2, ENST00000374940.3, HLA-DQA2 , ICRF6c-DV19.1-001 , NM_020056, Q76NI6, Q76NI6_HUMAN, uc318lyc.1, uc318lyc.2
UCSC ID: ENST00000374940.4_4
RefSeq Accession: NM_020056.5

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.