Non-C. elegans RefSeq Gene
 

Non-C. elegans RefSeq Gene CHMP4A

RefSeq: NM_014169.5   Status: Validated
Description: Homo sapiens charged multivesicular body protein 4A (CHMP4A), mRNA.
Organism: Homo sapiens
UCSC browser: NM_014169 on Human (hg38)
CDS: completeness unknown
OMIM: 610051
Entrez Gene: 29082
PubMed on Gene: CHMP4A
PubMed on Product: charged multivesicular body protein 4a

Summary of CHMP4A

CHMP4A belongs to the chromatin-modifying protein/charged multivesicular body protein (CHMP) family. These proteins are components of ESCRT-III (endosomal sorting complex required for transport III), a complex involved in degradation of surface receptor proteins and formation of endocytic multivesicular bodies (MVBs). Some CHMPs have both nuclear and cytoplasmic/vesicular distributions, and one such CHMP, CHMP1A (MIM 164010), is required for both MVB formation and regulation of cell cycle progression (Tsang et al., 2006 [PubMed 16730941]).[supplied by OMIM, Mar 2008]. CCDS Note: The coding region has been updated to shorten the N-terminus to one that is more supported by available conservation or experimental data.


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 |   456   64.5%         II     ++   6589711   6590558             NM_014169    50   559   980
browser |   264   66.7%          V     ++   7850035   7850658             NM_014169   101   376   980

Position: chrII:6589711-6590558
Genomic Size: 848
Strand: +
Gene Symbol: CHMP4A
CDS Start: complete
CDS End: not complete

Position: chrV:7850035-7850658
Genomic Size: 624
Strand: +
Gene Symbol: CHMP4A
CDS Start: not complete
CDS End: not complete

Links to sequence:

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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 C. elegans, 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 C. elegans 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