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RefSeq Gene
 

RefSeq Gene TNXB

RefSeq: NM_019105.7   Status: Reviewed
CDS: full length
OMIM: 600985
Entrez Gene: 7148
PubMed on Gene: TNXB
PubMed on Product: tenascin-X isoform 1 precursor
GeneCards: TNXB
AceView: TNXB
Stanford SOURCE: NM_019105

Summary of TNXB

This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The tenascins have anti-adhesive effects, as opposed to fibronectin which is adhesive. This protein is thought to function in matrix maturation during wound healing, and its deficiency has been associated with the connective tissue disorder Ehlers-Danlos syndrome. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. It is one of four genes in this cluster which have been duplicated. The duplicated copy of this gene is incomplete and is a pseudogene which is transcribed but does not encode a protein. The structure of this gene is unusual in that it overlaps the CREBL1 and CYP21A2 genes at its 5' and 3' ends, respectively. Multiple transcript variants encoding different isoforms have been found for this gene. [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 | 13125  100.0%          6     -  32008932  32077151             NM_019105     1 13125 13143
browser | 13125  100.0%  6_cox_hap2     -   3479583   3547813             NM_019105     1 13125 13143
browser | 13125  100.0%  6_dbb_hap3     -   3288148   3356325             NM_019105     1 13125 13143
browser |  6852  100.0%  6_mann_hap4     -   3375419   3408829             NM_019105   192  7043 13143
browser | 13125  100.0%  6_mcf_hap5     -   3388773   3456979             NM_019105     1 13125 13143
browser | 10147  100.0%  6_qbl_hap6     -   3269986   3314921             NM_019105  2979 13125 13143
browser |  6743   99.9%  6_ssto_hap7     -   3341640   3368931             NM_019105  6383 13125 13143

Position: chr6_mann_hap4:3375419-3408829
Genomic Size: 33411
Strand: -
Gene Symbol: TNXB
CDS Start: complete
CDS End: not complete

Position: chr6:32008932-32077151
Band: 6p21.33
Genomic Size: 68220
Strand: -
Gene Symbol: TNXB
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:3479583-3547813
Genomic Size: 68231
Strand: -
Gene Symbol: TNXB
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:3388773-3456979
Genomic Size: 68207
Strand: -
Gene Symbol: TNXB
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:3269986-3314921
Genomic Size: 44936
Strand: -
Gene Symbol: TNXB
CDS Start: not complete
CDS End: complete

Position: chr6_ssto_hap7:3341640-3368931
Genomic Size: 27292
Strand: -
Gene Symbol: TNXB
CDS Start: not complete
CDS End: complete

Position: chr6_dbb_hap3:3288148-3356325
Genomic Size: 68178
Strand: -
Gene Symbol: TNXB
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.