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RefSeq Gene
 

RefSeq Gene MICA

RefSeq: NM_000247.2   Status: Reviewed
CDS: 3' complete
OMIM: 600169
Entrez Gene: 100507436
PubMed on Gene: MICA
PubMed on Product: MHC class I polypeptide-related sequence A isoform 1 (MICA*001) precursor
GeneCards: MICA
AceView: MICA
Stanford SOURCE: NM_000247

Summary of MICA

MICA encodes the higly polymorphic MHC (HLA) class I chain-related gene A. The protein product is expressed on the cell surface, although unlike canonical class I molecules does not seem to associate with beta-2-microglobulin. It is thought that MICA functions as a stress-induced antigen that is broadly recognized by intestinal epithelial gamma delta T cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2010].


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 |  1365   98.4%  6_ssto_hap7     +   2705168   2716888             NM_000247     1  1365  1365
browser |  1365   98.5%  6_mann_hap4     +   2717805   2729520             NM_000247     1  1365  1365
browser |  1365  100.0%  6_qbl_hap6     +   2664817   2676634             NM_000247     1  1365  1365
browser |  1365   98.4%  6_cox_hap2     +   2884070   2895790             NM_000247     1  1365  1365
browser |  1365   98.4%          6     +  31371371  31383090             NM_000247     1  1365  1365

Position: chr6_ssto_hap7:2705168-2716888
Genomic Size: 11721
Strand: +
Gene Symbol: MICA
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:2884070-2895790
Genomic Size: 11721
Strand: +
Gene Symbol: MICA
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:2664817-2676634
Genomic Size: 11818
Strand: +
Gene Symbol: MICA
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:2717805-2729520
Genomic Size: 11716
Strand: +
Gene Symbol: MICA
CDS Start: complete
CDS End: complete

Position: chr6:31371371-31383090
Band: 6p21.33
Genomic Size: 11720
Strand: +
Gene Symbol: MICA
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.