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RefSeq Gene
 

RefSeq Gene SKIV2L

RefSeq: NM_006929.4   Status: Reviewed
CDS: full length
OMIM: 600478
Entrez Gene: 6499
PubMed on Gene: SKIV2L
PubMed on Product: helicase SKI2W
GeneCards: SKIV2L
AceView: SKIV2L
Stanford SOURCE: NM_006929

Summary of SKIV2L

DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a human homologue of yeast SKI2 and may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. This gene is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: U09877.1, Z48796.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025081, ERS025082 [ECO:0000348] ##Evidence-Data-END##


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 |  4170  100.0%          6     +  31926581  31937532             NM_006929     1  4170  4187
browser |  4170  100.0%  6_cox_hap2     +   3436337   3447288             NM_006929     1  4170  4187
browser |  4170  100.0%  6_dbb_hap3     +   3212164   3223115             NM_006929     1  4170  4187
browser |  4170  100.0%  6_mcf_hap5     +   3306425   3317376             NM_006929     1  4170  4187
browser |  4170  100.0%  6_qbl_hap6     +   3220370   3231321             NM_006929     1  4170  4187
browser |  4170  100.0%  6_ssto_hap7     +   3259291   3270242             NM_006929     1  4170  4187

Position: chr6:31926581-31937532
Band: 6p21.33
Genomic Size: 10952
Strand: +
Gene Symbol: SKIV2L
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:3259291-3270242
Genomic Size: 10952
Strand: +
Gene Symbol: SKIV2L
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:3220370-3231321
Genomic Size: 10952
Strand: +
Gene Symbol: SKIV2L
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:3306425-3317376
Genomic Size: 10952
Strand: +
Gene Symbol: SKIV2L
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:3436337-3447288
Genomic Size: 10952
Strand: +
Gene Symbol: SKIV2L
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:3212164-3223115
Genomic Size: 10952
Strand: +
Gene Symbol: SKIV2L
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.