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VCX variable charge X-linked [ Homo sapiens (human) ]

Gene ID: 26609, updated on 26-Oct-2022

Summary

Official Symbol
VCXprovided by HGNC
Official Full Name
variable charge X-linkedprovided by HGNC
Primary source
HGNC:HGNC:12667
See related
Ensembl:ENSG00000182583 MIM:300229; AllianceGenome:HGNC:12667
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VCX1; VCXB1; VCX-B1; VCX10R; VCX-10r
Summary
This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members are nuclear proteins. This gene contains 10 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]
Expression
Restricted expression toward testis (RPKM 23.7) See more
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Genomic context

See VCX in Genome Data Viewer
Location:
Xp22.31
Exon count:
3
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (7842262..7844143)
110 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (7395939..7397760)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (7810303..7812184)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5189 Neighboring gene steroid sulfatase Neighboring gene uncharacterized LOC124905241 Neighboring gene uncharacterized LOC107985675 Neighboring gene Sharpr-MPRA regulatory region 2843 Neighboring gene patatin like phospholipase domain containing 4

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC118975, MGC118976

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chromatin organization TAS
Traceable Author Statement
more info
PubMed 
involved_in ribosome assembly NAS
Non-traceable Author Statement
more info
PubMed 
involved_in spermatogenesis TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
variable charge X-linked protein 1
Names
variable charge protein on X with ten repeats
variable charge, X chromosome
variably charged protein X-B1

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_001393662.1NP_001380591.1  variable charge X-linked protein 1

    Status: REVIEWED

    Source sequence(s)
    AC005296
    Consensus CDS
    CCDS14128.1
    UniProtKB/Swiss-Prot
    Q9P0H3
    Related
    ENSP00000509688.1, ENST00000688183.1
    Conserved Domains (2) summary
    PTZ00341
    Location:78192
    PTZ00341; Ring-infected erythrocyte surface antigen; Provisional
    pfam15231
    Location:1129
    VCX_VCY; Variable charge X/Y family
  2. NM_013452.3NP_038480.2  variable charge X-linked protein 1

    See identical proteins and their annotated locations for NP_038480.2

    Status: REVIEWED

    Source sequence(s)
    AC005296
    Consensus CDS
    CCDS14128.1
    UniProtKB/Swiss-Prot
    Q9H320, Q9P0H3
    Related
    ENSP00000370447.3, ENST00000381059.7
    Conserved Domains (2) summary
    PTZ00341
    Location:78192
    PTZ00341; Ring-infected erythrocyte surface antigen; Provisional
    pfam15231
    Location:1129
    VCX_VCY; Variable charge X/Y family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    7842262..7844143
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545490.4XP_011543792.1  variable charge X-linked protein 1 isoform X1

    Related
    ENSP00000508920.1, ENST00000692567.1
    Conserved Domains (1) summary
    pfam15231
    Location:1141
    VCX_VCY; Variable charge X/Y family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    7395939..7397760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)