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RefSeq Gene
 

RefSeq Gene RNF39

RefSeq: NM_170769.2   Status: Validated
CDS: 3' complete
OMIM: 607524
Entrez Gene: 80352
PubMed on Gene: RNF39
PubMed on Product: RING finger protein 39 isoform 2
GeneCards: RNF39
AceView: RNF39
Stanford SOURCE: NM_170769

Summary of RNF39

This gene lies within the major histocompatibility complex class I region on chromosome 6. Studies of a similar rat protein suggest that this gene encodes a protein that plays a role in an early phase of synaptic plasticity. 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 |  1970  100.0%          6     -  30038043  30043626             NM_170769     1  1970  1970
browser |  1970  100.0%  6_apd_hap1     -   1278274   1283857             NM_170769     1  1970  1970
browser |  1970   99.9%  6_cox_hap2     -   1550143   1555726             NM_170769     1  1970  1970
browser |  1970  100.0%  6_dbb_hap3     -   1331767   1337350             NM_170769     1  1970  1970
browser |  1970  100.0%  6_mann_hap4     -   1336636   1342219             NM_170769     1  1970  1970
browser |  1970  100.0%  6_mcf_hap5     -   1419941   1425524             NM_170769     1  1970  1970
browser |  1965   99.6%  6_qbl_hap6     -   1331022   1336600             NM_170769     1  1970  1970
browser |  1970  100.0%  6_ssto_hap7     -   1368483   1374066             NM_170769     1  1970  1970

Position: chr6_dbb_hap3:1331767-1337350
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6_apd_hap1:1278274-1283857
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6_mann_hap4:1336636-1342219
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6_mcf_hap5:1419941-1425524
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6_qbl_hap6:1331022-1336600
Genomic Size: 5579
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6_ssto_hap7:1368483-1374066
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6_cox_hap2:1550143-1555726
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
CDS Start: complete
CDS End: complete

Position: chr6:30038043-30043626
Band: 6p22.1
Genomic Size: 5584
Strand: -
Gene Symbol: RNF39
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.