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RefSeq Gene
 

RefSeq Gene HLA-DPA1

RefSeq: NM_001242525.1   Status: Reviewed
CDS: 3' complete
OMIM: 142880
Entrez Gene: 3113
PubMed on Gene: HLA-DPA1
PubMed on Product: HLA class II histocompatibility antigen DP alpha 1 chain precursor
GeneCards: HLA-DPA1
AceView: HLA-DPA1
Stanford SOURCE: NM_001242525

Summary of HLA-DPA1

HLA-DPA1 belongs to the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DPA) and a beta (DPB) chain, both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa and its gene contains 5 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DP molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to 4 different molecules. [provided by RefSeq, Jul 2008].


mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |  1696  100.0%  6_ssto_hap7     -   4512850   4529059          NM_001242525     1  1696  1712
browser |  1696  100.0%  6_apd_hap1     -   4319165   4335362          NM_001242525     1  1696  1712
browser |  1696  100.0%          6     -  33032346  33048555          NM_001242525     1  1696  1712
browser |  1687   99.9%  6_cox_hap2     -   4476526   4492734          NM_001242525     1  1696  1712
browser |  1696  100.0%  6_dbb_hap3     -   4313685   4329894          NM_001242525     1  1696  1712
browser |  1696   99.9%  6_mann_hap4     -   4489886   4506101          NM_001242525     1  1696  1712
browser |  1696  100.0%  6_mcf_hap5     -   4369219   4385416          NM_001242525     1  1696  1712
browser |  1696   99.8%  6_qbl_hap6     -   4264797   4281012          NM_001242525     1  1696  1712

Position: chr6_apd_hap1:4319165-4335362
Genomic Size: 16198
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6:33032346-33048555
Band: 6p21.32
Genomic Size: 16210
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:4476526-4492734
Genomic Size: 16209
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:4313685-4329894
Genomic Size: 16210
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:4489886-4506101
Genomic Size: 16216
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:4369219-4385416
Genomic Size: 16198
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:4264797-4281012
Genomic Size: 16216
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:4512850-4529059
Genomic Size: 16210
Strand: -
Gene Symbol: HLA-DPA1
CDS Start: complete
CDS End: complete

Links to sequence:

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Data last updated: 2013-05-15

Description

The RefSeq Genes track shows known human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated daily.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark).

The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. This page is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

  • Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely.
  • Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.
  • Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box.

Methods

RefSeq RNAs were aligned against the human genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.