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RefSeq Gene
 

RefSeq Gene HLA-C

RefSeq: NM_002117.5   Status: Reviewed
CDS: 3' complete
OMIM: 142840
Entrez Gene: 3107
PubMed on Gene: HLA-C
PubMed on Product: HLA class I histocompatibility antigen Cw-1 alpha chain precursor
GeneCards: HLA-C
AceView: HLA-C
Stanford SOURCE: NM_002117

Summary of HLA-C

HLA-C belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Over one hundred HLA-C alleles have been described [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 |  1586  100.0%          6     -  31236526  31239913             NM_002117     1  1586  1586
browser |  1586   99.8%  6_cox_hap2     -   2749781   2753168             NM_002117     1  1586  1586
browser |  1568   97.2%  6_dbb_hap3     -   2532134   2535511             NM_002117     1  1586  1586
browser |  1574   96.7%  6_mann_hap4     -   2583421   2586798             NM_002117     1  1586  1586
browser |  1585   96.3%  6_mcf_hap5     -   2617063   2620440             NM_002117     1  1586  1586
browser |  1568   96.5%  6_qbl_hap6     -   2529777   2533154             NM_002117     1  1586  1586
browser |  1568   96.5%  6_ssto_hap7     -   2570005   2573382             NM_002117     1  1586  1586

Position: chr6_cox_hap2:2749781-2753168
Genomic Size: 3388
Strand: -
Gene Symbol: HLA-C
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:2532134-2535511
Genomic Size: 3378
Strand: -
Gene Symbol: HLA-C
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:2583421-2586798
Genomic Size: 3378
Strand: -
Gene Symbol: HLA-C
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:2570005-2573382
Genomic Size: 3378
Strand: -
Gene Symbol: HLA-C
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:2529777-2533154
Genomic Size: 3378
Strand: -
Gene Symbol: HLA-C
CDS Start: complete
CDS End: complete

Position: chr6:31236526-31239913
Band: 6p21.33
Genomic Size: 3388
Strand: -
Gene Symbol: HLA-C
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:2617063-2620440
Genomic Size: 3378
Strand: -
Gene Symbol: HLA-C
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.