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RefSeq Gene
 

RefSeq Gene LTA

RefSeq: NM_000595.3   Status: Reviewed
CDS: 3' complete
OMIM: 153440
Entrez Gene: 4049
PubMed on Gene: LTA
PubMed on Product: lymphotoxin-alpha precursor
GeneCards: LTA
AceView: LTA
Stanford SOURCE: NM_000595

Summary of LTA

The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012].


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 |  1410  100.0%  6_ssto_hap7     +   2870872   2872901             NM_000595     1  1410  1423
browser |  1410  100.0%          6     +  31540071  31542100             NM_000595     1  1410  1423
browser |  1409   99.9%  6_cox_hap2     +   3049688   3051716             NM_000595     2  1410  1423
browser |  1410   99.9%  6_dbb_hap3     +   2825610   2827641             NM_000595     1  1410  1423
browser |  1410  100.0%  6_mann_hap4     +   2882955   2884984             NM_000595     1  1410  1423
browser |  1410   99.9%  6_mcf_hap5     +   2919775   2921806             NM_000595     1  1410  1423
browser |  1410   99.9%  6_qbl_hap6     +   2833707   2835738             NM_000595     1  1410  1423

Position: chr6_cox_hap2:3049688-3051716
Genomic Size: 2029
Strand: +
Gene Symbol: LTA
CDS Start: complete
CDS End: complete

Position: chr6:31540071-31542100
Band: 6p21.33
Genomic Size: 2030
Strand: +
Gene Symbol: LTA
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:2833707-2835738
Genomic Size: 2032
Strand: +
Gene Symbol: LTA
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:2882955-2884984
Genomic Size: 2030
Strand: +
Gene Symbol: LTA
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:2870872-2872901
Genomic Size: 2030
Strand: +
Gene Symbol: LTA
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:2825610-2827641
Genomic Size: 2032
Strand: +
Gene Symbol: LTA
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:2919775-2921806
Genomic Size: 2032
Strand: +
Gene Symbol: LTA
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.