Non-Zebrafish RefSeq Gene
 

Non-Zebrafish RefSeq Gene HTRA2

RefSeq: NR_135771.1   Status: Reviewed
Description: Homo sapiens HtrA serine peptidase 2 (HTRA2), transcript variant 7, non-coding RNA.
Organism: Homo sapiens
UCSC browser: NR_135771 on Human (hg38)
CDS: completeness unknown
OMIM: 606441
Entrez Gene: 27429
PubMed on Gene: HTRA2

Summary of HTRA2

This gene encodes a serine protease. The protein has been localized in the endoplasmic reticulum and interacts with an alternatively spliced form of mitogen-activated protein kinase 14. The protein has also been localized to the mitochondria with release to the cytosol following apoptotic stimulus. The protein is thought to induce apoptosis by binding the apoptosis inhibitory protein baculoviral IAP repeat-containing 4. Nuclear localization of this protein has also been observed. Alternate splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.


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 |   684   68.3%         10     ++  34128868  34295401             NR_135771   553  1293  2002
browser |   501   69.5%         10     ++  34091834  34114366             NR_135771   769  1293  2002
browser |   696   67.9%         13     +-   8671240   8773055             NR_135771   553  1293  2002
browser |   696   68.0%         13     +-   8930366   8963874             NR_135771   553  1293  2002

Position: chr10:34091834-34114366
Genomic Size: 22533
Strand: +
Gene Symbol: HTRA2

Position: chr10:34128868-34295401
Genomic Size: 166534
Strand: +
Gene Symbol: HTRA2

Position: chr13:8671240-8773055
Genomic Size: 101816
Strand: -
Gene Symbol: HTRA2

Position: chr13:8930366-8963874
Genomic Size: 33509
Strand: -
Gene Symbol: HTRA2

Links to sequence:

  • Non-protein coding gene or gene fragment, no protein prediction available.
  • mRNA Sequence (may be different from the genomic sequence)
  • Genomic Sequence from assembly
View table schema

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Data last updated at UCSC: 2020-08-18

Description

This track shows known protein-coding and non-protein-coding genes for organisms other than zebrafish, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly.

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.

  • 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.
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Methods

The RNAs were aligned against the zebrafish 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 0.5% of the best and at least 25% 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. PMID: 11932250; PMC: PMC187518

Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018

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. PMID: 15608248; PMC: PMC539979