Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CBX4 (chromobox 4)

Identity

Alias (NCBI)NBP16
PC2
HGNC (Hugo) CBX4
HGNC Alias symbhPC2
PC2
NBP16
HGNC Alias nameNS5ATP1-binding protein 16
 Pc class 2 homolog (Drosophila)
HGNC Previous namechromobox homolog 4 (Drosophila Pc class)
 chromobox homolog 4
LocusID (NCBI) 8535
Atlas_Id 46645
Location 17q25.3  [Link to chromosome band 17q25]
Location_base_pair Starts at 79833156 and ends at 79839440 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CBX4 (17q25.3) / DBI (2q14.2)CBX4 (17q25.3) / EFCAB5 (17q11.2)CBX4 (17q25.3) / RFK (9q21.13)
CBX4 17q25.3 / EFCAB5 17q11.2CBX4 17q25.3 / RFK 9q21.13

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 



External links

 

Nomenclature
HGNC (Hugo)CBX4   1554
Cards
Entrez_Gene (NCBI)CBX4    chromobox 4
AliasesNBP16; PC2
GeneCards (Weizmann)CBX4
Ensembl hg19 (Hinxton)ENSG00000141582 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000141582 [Gene_View]  ENSG00000141582 [Sequence]  chr17:79833156-79839440 [Contig_View]  CBX4 [Vega]
ICGC DataPortalENSG00000141582
TCGA cBioPortalCBX4
AceView (NCBI)CBX4
Genatlas (Paris)CBX4
SOURCE (Princeton)CBX4
Genetics Home Reference (NIH)CBX4
Genomic and cartography
GoldenPath hg38 (UCSC)CBX4  -     chr17:79833156-79839440 -  17q25.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CBX4  -     17q25.3   [Description]    (hg19-Feb_2009)
GoldenPathCBX4 - 17q25.3 [CytoView hg19]  CBX4 - 17q25.3 [CytoView hg38]
ImmunoBaseENSG00000141582
Genome Data Viewer NCBICBX4 [Mapview hg19]  
OMIM603079   
Gene and transcription
Genbank (Entrez)AF013956 AI796748 AY390430 BC014967 BG029608
RefSeq transcript (Entrez)NM_003655
Consensus coding sequences : CCDS (NCBI)CBX4
Gene ExpressionCBX4 [ NCBI-GEO ]   CBX4 [ EBI - ARRAY_EXPRESS ]   CBX4 [ SEEK ]   CBX4 [ MEM ]
Gene Expression Viewer (FireBrowse)CBX4 [ Firebrowse - Broad ]
GenevisibleExpression of CBX4 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8535
GTEX Portal (Tissue expression)CBX4
Human Protein AtlasENSG00000141582-CBX4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00257   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00257  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00257
Catalytic activity : Enzyme2.3.2.- [ Enzyme-Expasy ]   2.3.2.-2.3.2.- [ IntEnz-EBI ]   2.3.2.- [ BRENDA ]   2.3.2.- [ KEGG ]   [ MEROPS ]
PhosPhoSitePlusO00257
Domaine pattern : Prosite (Expaxy)CHROMO_1 (PS00598)    CHROMO_2 (PS50013)   
Domains : Interpro (EBI)CBX4    CBX7_C    Chromo-like_dom_sf    Chromo/chromo_shadow_dom    Chromo_dom_subgr    Chromo_domain    Chromodomain_CS   
Domain families : Pfam (Sanger)CBX7_C (PF17218)    Chromo (PF00385)   
Domain families : Pfam (NCBI)pfam17218    pfam00385   
Domain families : Smart (EMBL)CHROMO (SM00298)  
Conserved Domain (NCBI)CBX4
PDB (RSDB)2K28    3I8Z    5EPL   
PDB Europe2K28    3I8Z    5EPL   
PDB (PDBSum)2K28    3I8Z    5EPL   
PDB (IMB)2K28    3I8Z    5EPL   
Structural Biology KnowledgeBase2K28    3I8Z    5EPL   
SCOP (Structural Classification of Proteins)2K28    3I8Z    5EPL   
CATH (Classification of proteins structures)2K28    3I8Z    5EPL   
SuperfamilyO00257
AlphaFold pdb e-kbO00257   
Human Protein Atlas [tissue]ENSG00000141582-CBX4 [tissue]
HPRD04357
Protein Interaction databases
DIP (DOE-UCLA)O00257
IntAct (EBI)O00257
BioGRIDCBX4
STRING (EMBL)CBX4
ZODIACCBX4
Ontologies - Pathways
QuickGOO00257
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  transcription cis-regulatory region binding  chromatin binding  transcription corepressor activity  single-stranded RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  chromatin organization  nuclear body  nuclear speck  protein sumoylation  SUMO transferase activity  enzyme binding  PcG protein complex  SUMO binding  methylated histone binding  PRC1 complex  negative regulation of apoptotic process  negative regulation of transcription, DNA-templated  phosphoprotein binding  SUMO ligase activity  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  transcription cis-regulatory region binding  chromatin binding  transcription corepressor activity  single-stranded RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  chromatin organization  nuclear body  nuclear speck  protein sumoylation  SUMO transferase activity  enzyme binding  PcG protein complex  SUMO binding  methylated histone binding  PRC1 complex  negative regulation of apoptotic process  negative regulation of transcription, DNA-templated  phosphoprotein binding  SUMO ligase activity  
Pathways : BIOCARTAThe PRC2 Complex Sets Long-term Gene Silencing Through Modification of Histone Tails [Genes]   
NDEx NetworkCBX4
Atlas of Cancer Signalling NetworkCBX4
Wikipedia pathwaysCBX4
Orthology - Evolution
OrthoDB8535
GeneTree (enSembl)ENSG00000141582
Phylogenetic Trees/Animal Genes : TreeFamCBX4
Homologs : HomoloGeneCBX4
Homology/Alignments : Family Browser (UCSC)CBX4
Gene fusions - Rearrangements
Fusion : MitelmanCBX4/EFCAB5 [17q25.3/17q11.2]  
Fusion : MitelmanCBX4/RFK [17q25.3/9q21.13]  
Fusion : QuiverCBX4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCBX4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CBX4
dbVarCBX4
ClinVarCBX4
MonarchCBX4
1000_GenomesCBX4 
Exome Variant ServerCBX4
GNOMAD BrowserENSG00000141582
Varsome BrowserCBX4
ACMGCBX4 variants
VarityO00257
Genomic Variants (DGV)CBX4 [DGVbeta]
DECIPHERCBX4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCBX4 
Mutations
ICGC Data PortalCBX4 
TCGA Data PortalCBX4 
Broad Tumor PortalCBX4
OASIS PortalCBX4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCBX4  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DCBX4
Mutations and Diseases : HGMDCBX4
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaCBX4
DgiDB (Drug Gene Interaction Database)CBX4
DoCM (Curated mutations)CBX4
CIViC (Clinical Interpretations of Variants in Cancer)CBX4
Cancer3DCBX4
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603079   
Orphanet
DisGeNETCBX4
MedgenCBX4
Genetic Testing Registry CBX4
NextProtO00257 [Medical]
GENETestsCBX4
Target ValidationCBX4
Huge Navigator CBX4 [HugePedia]
ClinGenCBX4
Clinical trials, drugs, therapy
MyCancerGenomeCBX4
Protein Interactions : CTDCBX4
Pharm GKB GenePA26129
PharosO00257
Clinical trialCBX4
Miscellaneous
canSAR (ICR)CBX4
HarmonizomeCBX4
DataMed IndexCBX4
Probes
Litterature
PubMed109 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXCBX4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Mon Oct 4 15:02:25 CEST 2021

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