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RefSeq Gene
 

RefSeq Gene C2

RefSeq: NM_000063.5   Status: Reviewed
CDS: 3' complete
OMIM: 613927
Entrez Gene: 717
PubMed on Gene: C2
PubMed on Product: complement C2 isoform 1 preproprotein
GeneCards: C2
AceView: C2
Stanford SOURCE: NM_000063

Summary of C2

Component C2 is a serum glycoprotein that functions as part of the classical pathway of the complement system. Activated C1 cleaves C2 into C2a and C2b. The serine proteinase C2a then combines with complement factor 4b to create the C3 or C5 convertase. Deficiency of C2 has been reported to associated with certain autoimmune diseases and SNPs in this gene have been associated with altered susceptibility to age-related macular degeneration. This gene localizes within the class III region of the MHC on the short arm of chromosome 6. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described in publications but their full-length sequence has not been determined.[provided by RefSeq, Mar 2009].


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 |  2838  100.0%  6_ssto_hap7     +   3228026   3246159             NM_000063     1  2838  2867
browser |  2838  100.0%          6     +  31895266  31913449             NM_000063     1  2838  2867
browser |  2838  100.0%  6_cox_hap2     +   3405022   3423205             NM_000063     1  2838  2867
browser |  2838  100.0%  6_dbb_hap3     +   3180853   3199037             NM_000063     1  2838  2867
browser |  2838  100.0%  6_mann_hap4     +   3238324   3256269             NM_000063     1  2838  2867
browser |  2838  100.0%  6_mcf_hap5     +   3275161   3293293             NM_000063     1  2838  2867
browser |  2838  100.0%  6_qbl_hap6     +   3189059   3207243             NM_000063     1  2838  2867

Position: chr6_dbb_hap3:3180853-3199037
Genomic Size: 18185
Strand: +
Gene Symbol: C2
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:3189059-3207243
Genomic Size: 18185
Strand: +
Gene Symbol: C2
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:3275161-3293293
Genomic Size: 18133
Strand: +
Gene Symbol: C2
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:3405022-3423205
Genomic Size: 18184
Strand: +
Gene Symbol: C2
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:3228026-3246159
Genomic Size: 18134
Strand: +
Gene Symbol: C2
CDS Start: complete
CDS End: complete

Position: chr6:31895266-31913449
Band: 6p21.33
Genomic Size: 18184
Strand: +
Gene Symbol: C2
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:3238324-3256269
Genomic Size: 17946
Strand: +
Gene Symbol: C2
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.