Genomes Genome Browser Tables Help  
RefSeq Gene
 

RefSeq Gene COL11A2

RefSeq: NM_080681.2   Status: Reviewed
CDS: full length
OMIM: 120290
Entrez Gene: 1302
PubMed on Gene: COL11A2
PubMed on Product: collagen alpha-2(XI) chain isoform 2 preproprotein
GeneCards: COL11A2
AceView: COL11A2
Stanford SOURCE: NM_080681

Summary of COL11A2

This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6. [provided by RefSeq, Jul 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 |  6167  100.0%          6     -  33130469  33160245             NM_080681     1  6167  6167
browser |  6167  100.0%  6_cox_hap2     -   4574306   4604081             NM_080681     1  6167  6167
browser |  6167  100.0%  6_dbb_hap3     -   4411776   4441552             NM_080681     1  6167  6167
browser |  6167  100.0%  6_mann_hap4     -   4587785   4617560             NM_080681     1  6167  6167
browser |  6167  100.0%  6_mcf_hap5     -   4604235   4634009             NM_080681     1  6167  6167
browser |  6167  100.0%  6_qbl_hap6     -   4362692   4392467             NM_080681     1  6167  6167
browser |  5860  100.0%  6_ssto_hap7     -   4610636   4637414             NM_080681   308  6167  6167

Position: chr6:33130469-33160245
Band: 6p21.32
Genomic Size: 29777
Strand: -
Gene Symbol: COL11A2
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:4587785-4617560
Genomic Size: 29776
Strand: -
Gene Symbol: COL11A2
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:4411776-4441552
Genomic Size: 29777
Strand: -
Gene Symbol: COL11A2
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:4362692-4392467
Genomic Size: 29776
Strand: -
Gene Symbol: COL11A2
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:4610636-4637414
Genomic Size: 26779
Strand: -
Gene Symbol: COL11A2
CDS Start: not complete
CDS End: complete

Position: chr6_mcf_hap5:4604235-4634009
Genomic Size: 29775
Strand: -
Gene Symbol: COL11A2
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:4574306-4604081
Genomic Size: 29776
Strand: -
Gene Symbol: COL11A2
CDS Start: complete
CDS End: complete

Links to sequence:

View table schema

Go to RefSeq Genes track controls

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.