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RefSeq Gene
 

RefSeq Gene TRIM39

RefSeq: NM_172016.2   Status: Reviewed
CDS: 3' complete
OMIM: 605700
Entrez Gene: 56658
PubMed on Gene: TRIM39
PubMed on Product: E3 ubiquitin-protein ligase TRIM39 isoform 2
GeneCards: TRIM39
AceView: TRIM39
Stanford SOURCE: NM_172016

Summary of TRIM39

The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms. [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 |  3563  100.0%          6     +  30295008  30311506             NM_172016     1  3563  3578
browser |  3563  100.0%  6_apd_hap1     +   1606637   1623141             NM_172016     1  3563  3578
browser |  3563  100.0%  6_cox_hap2     +   1807014   1823516             NM_172016     1  3563  3578
browser |  3563  100.0%  6_dbb_hap3     +   1588656   1605160             NM_172016     1  3563  3578
browser |  3563  100.0%  6_mann_hap4     +   1643076   1659580             NM_172016     1  3563  3578
browser |  3563  100.0%  6_qbl_hap6     +   1587902   1604407             NM_172016     1  3563  3578
browser |  3563  100.0%  6_ssto_hap7     +   1624983   1641484             NM_172016     1  3563  3578

Position: chr6_qbl_hap6:1587902-1604407
Genomic Size: 16506
Strand: +
Gene Symbol: TRIM39
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:1624983-1641484
Genomic Size: 16502
Strand: +
Gene Symbol: TRIM39
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:1807014-1823516
Genomic Size: 16503
Strand: +
Gene Symbol: TRIM39
CDS Start: complete
CDS End: complete

Position: chr6_dbb_hap3:1588656-1605160
Genomic Size: 16505
Strand: +
Gene Symbol: TRIM39
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:1643076-1659580
Genomic Size: 16505
Strand: +
Gene Symbol: TRIM39
CDS Start: complete
CDS End: complete

Position: chr6:30295008-30311506
Band: 6p22.1
Genomic Size: 16499
Strand: +
Gene Symbol: TRIM39
CDS Start: complete
CDS End: complete

Position: chr6_apd_hap1:1606637-1623141
Genomic Size: 16505
Strand: +
Gene Symbol: TRIM39
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.