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RNF103-CHMP3 RNF103-CHMP3 readthrough [ Homo sapiens (human) ]

Gene ID: 100526767, updated on 10-Oct-2023

Summary

Official Symbol
RNF103-CHMP3provided by HGNC
Official Full Name
RNF103-CHMP3 readthroughprovided by HGNC
Primary source
HGNC:HGNC:38847
See related
Ensembl:ENSG00000249884 AllianceGenome:HGNC:38847
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NEDF; CHMP3; VPS24; CGI149; hVps24; RNF103-VPS24
Summary
This locus represents naturally occurring read-through transcription between the neighboring RNF103 (ring finger protein 103) and CHMP3 (charged multivesicular body protein 3) genes. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in esophagus (RPKM 39.0), thyroid (RPKM 37.6) and 25 other tissues See more
Orthologs
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Genomic context

See RNF103-CHMP3 in Genome Data Viewer
Location:
2p11.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86503430..86721122, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86505444..86723107, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86730553..86948245, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene U8 small nucleolar RNA Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:86667563-86668106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16161 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:86708929-86710128 Neighboring gene lysine demethylase 3A Neighboring gene MPRA-validated peak3779 silencer Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59439 Neighboring gene charged multivesicular body protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16163 Neighboring gene Sharpr-MPRA regulatory region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16164 Neighboring gene CHMP3 and RNF103 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11715 Neighboring gene Sharpr-MPRA regulatory region 3990 Neighboring gene uncharacterized LOC124907853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86859935-86860458 Neighboring gene ring finger protein 103 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:86921806-86923005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:86946607-86947140 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86947334-86947492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86952106-86952606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86952607-86953107 Neighboring gene required for meiotic nuclear division 5 homolog A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16165 Neighboring gene CD8A intronic regulatory region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:87016737-87017571 Neighboring gene uncharacterized LOC105374846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11721 Neighboring gene MPRA-validated peak3783 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87066785-87067341 Neighboring gene CD8 subunit alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87083199-87083700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87083701-87084200 Neighboring gene CD8 subunit beta Neighboring gene ANAPC1 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General protein information

Preferred Names
RNF103-CHMP3 protein
Names
Charged multivesicular body protein 3
Chromatin-modifying protein 3
Neuroendocrine differentiation factor
RNF103-CHMP3 read-through
RNF103-VPS24 readthrough
Vacuolar protein sorting-associated protein 24

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001198954.1NP_001185883.1  RNF103-CHMP3 protein

    See identical proteins and their annotated locations for NP_001185883.1

    Status: VALIDATED

    Source sequence(s)
    AC015971, AC068288, AK294389
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000474823.1, ENST00000604011.5
    Conserved Domains (1) summary
    pfam03357
    Location:47216
    Snf7; Snf7

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    86503430..86721122 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86505444..86723107 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)