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CBX4 chromobox 4 [ Homo sapiens (human) ]

Gene ID: 8535, updated on 21-Dec-2019

Summary

Official Symbol
CBX4provided by HGNC
Official Full Name
chromobox 4provided by HGNC
Primary source
HGNC:HGNC:1554
See related
Ensembl:ENSG00000141582 MIM:603079
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
PC2; NBP16
Expression
Broad expression in bone marrow (RPKM 17.4), spleen (RPKM 5.9) and 24 other tissues See more
Orthologs

Genomic context

See CBX4 in Genome Data Viewer
Location:
17q25.3
Exon count:
6
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (79833156..79839440, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (77806955..77813222, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723961 Neighboring gene long intergenic non-protein coding RNA 1977 Neighboring gene long intergenic non-protein coding RNA 1979 Neighboring gene long intergenic non-protein coding RNA 1978 Neighboring gene TBC1 domain family member 16

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?

Phenotypes

NHGRI GWAS Catalog

Description
Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SUMO binding IDA
Inferred from Direct Assay
more info
PubMed 
SUMO transferase activity EXP
Inferred from Experiment
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
methylated histone binding IEA
Inferred from Electronic Annotation
more info
 
phosphoprotein binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded RNA binding IEA
Inferred from Electronic Annotation
more info
 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
transcription regulatory region DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
protein sumoylation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
PRC1 complex IDA
Inferred from Direct Assay
more info
PubMed 
PcG protein complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 SUMO-protein ligase CBX4
Names
NS5ATP1-binding protein 16
Pc class 2 homolog
chromobox homolog 4 (Pc class homolog, Drosophila)
chromobox protein homolog 4
chromobox-like protein 4
polycomb 2 homolog

NCBI Reference Sequences (RefSeq)

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_003655.3NP_003646.2  E3 SUMO-protein ligase CBX4

    See identical proteins and their annotated locations for NP_003646.2

    Status: VALIDATED

    Source sequence(s)
    AC100791, AF013956, AI796748, BC014967, BG029608, BQ225831
    Consensus CDS
    CCDS32758.1
    UniProtKB/Swiss-Prot
    O00257
    UniProtKB/TrEMBL
    A0A0S2Z5B2
    Related
    ENSP00000269397.4, ENST00000269397.9
    Conserved Domains (2) summary
    smart00298
    Location:1062
    CHROMO; Chromatin organization modifier domain
    pfam17218
    Location:538559
    CBX7_C; CBX family C-terminal motif

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    79833156..79839440 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525399.2XP_011523701.1  E3 SUMO-protein ligase CBX4 isoform X1

    Conserved Domains (1) summary
    pfam17218
    Location:472493
    CBX7_C; CBX family C-terminal motif
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