Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CBX5 (chromobox 5)

Identity

Alias_nameschromobox homolog 5 (Drosophila HP1 alpha)
chromobox homolog 5 (HP1 alpha homolog, Drosophila)
chromobox homolog 5
Alias_symbol (synonym)HP1Hs-alpha
HP1
HP1-ALPHA
Other aliasHEL25
HP1A
HGNC (Hugo) CBX5
LocusID (NCBI) 23468
Atlas_Id 45904
Location 12q13.13  [Link to chromosome band 12q13]
Location_base_pair Starts at 54230946 and ends at 54280131 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)
ACTB (7p22.1) / CBX5 (12q13.13)CBX5 (12q13.13) / NFE2 (12q13.13)CBX5 (12q13.13) / TFE3 (Xp11.23)
CBX5 (12q13.13) / ZSCAN5A (19q13.43)NAV2 (11p15.1) / CBX5 (12q13.13)PDIA4 (7q36.1) / CBX5 (12q13.13)
TMEM138 (11q12.2) / CBX5 (12q13.13)CBX5 12q13.13 / NFE2 12q13.13PDIA4 7q36.1 / CBX5 12q13.13

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

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(7;12)(q36;q13) PDIA4/CBX5
CBX5/NFE2 (12q13)


External links

Nomenclature
HGNC (Hugo)CBX5   1555
Cards
Entrez_Gene (NCBI)CBX5  23468  chromobox 5
AliasesHEL25; HP1; HP1A
GeneCards (Weizmann)CBX5
Ensembl hg19 (Hinxton)ENSG00000094916 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000094916 [Gene_View]  ENSG00000094916 [Sequence]  chr12:54230946-54280131 [Contig_View]  CBX5 [Vega]
ICGC DataPortalENSG00000094916
TCGA cBioPortalCBX5
AceView (NCBI)CBX5
Genatlas (Paris)CBX5
WikiGenes23468
SOURCE (Princeton)CBX5
Genetics Home Reference (NIH)CBX5
Genomic and cartography
GoldenPath hg38 (UCSC)CBX5  -     chr12:54230946-54280131 -  12q13.13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CBX5  -     12q13.13   [Description]    (hg19-Feb_2009)
EnsemblCBX5 - 12q13.13 [CytoView hg19]  CBX5 - 12q13.13 [CytoView hg38]
Mapping of homologs : NCBICBX5 [Mapview hg19]  CBX5 [Mapview hg38]
OMIM604478   
Gene and transcription
Genbank (Entrez)AF147443 AK023520 AK055641 AK056315 AK095108
RefSeq transcript (Entrez)NM_001127321 NM_001127322 NM_012117
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CBX5
Cluster EST : UnigeneHs.349283 [ NCBI ]
CGAP (NCI)Hs.349283
Alternative Splicing GalleryENSG00000094916
Gene ExpressionCBX5 [ NCBI-GEO ]   CBX5 [ EBI - ARRAY_EXPRESS ]   CBX5 [ SEEK ]   CBX5 [ MEM ]
Gene Expression Viewer (FireBrowse)CBX5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23468
GTEX Portal (Tissue expression)CBX5
Human Protein AtlasENSG00000094916-CBX5 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP45973   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP45973  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP45973
Splice isoforms : SwissVarP45973
PhosPhoSitePlusP45973
Domaine pattern : Prosite (Expaxy)CHROMO_1 (PS00598)    CHROMO_2 (PS50013)   
Domains : Interpro (EBI)Chromo-like_dom_sf    Chromo/chromo_shadow_dom    Chromo_dom_subgr    Chromo_domain    Chromo_shadow_dom    Chromodomain_CS   
Domain families : Pfam (Sanger)Chromo (PF00385)    Chromo_shadow (PF01393)   
Domain families : Pfam (NCBI)pfam00385    pfam01393   
Domain families : Smart (EMBL)CHROMO (SM00298)  ChSh (SM00300)  
Conserved Domain (NCBI)CBX5
DMDM Disease mutations23468
Blocks (Seattle)CBX5
PDB (SRS)3FDT    3I3C   
PDB (PDBSum)3FDT    3I3C   
PDB (IMB)3FDT    3I3C   
PDB (RSDB)3FDT    3I3C   
Structural Biology KnowledgeBase3FDT    3I3C   
SCOP (Structural Classification of Proteins)3FDT    3I3C   
CATH (Classification of proteins structures)3FDT    3I3C   
SuperfamilyP45973
Human Protein Atlas [tissue]ENSG00000094916-CBX5 [tissue]
Peptide AtlasP45973
HPRD05131
IPIIPI00024662   IPI01021488   IPI01021779   IPI00744855   
Protein Interaction databases
DIP (DOE-UCLA)P45973
IntAct (EBI)P45973
FunCoupENSG00000094916
BioGRIDCBX5
STRING (EMBL)CBX5
ZODIACCBX5
Ontologies - Pathways
QuickGOP45973
Ontology : AmiGOhistone deacetylase complex  negative regulation of transcription by RNA polymerase II  kinetochore  nuclear chromosome, telomeric region  chromatin binding  protein binding  nucleus  nuclear envelope  nucleoplasm  nuclear heterochromatin  pericentric heterochromatin  nucleolus  cellular response to DNA damage stimulus  blood coagulation  chromocenter  viral process  PML body  transcriptional repressor complex  protein binding, bridging  nuclear pericentric heterochromatin  protein-containing complex  methylated histone binding  histone methyltransferase complex  identical protein binding  protein homodimerization activity  histone deacetylase binding  ribonucleoprotein complex binding  protein-containing complex binding  negative regulation of transcription, DNA-templated  negative regulation of transcription, DNA-templated  negative regulation of G0 to G1 transition  repressing transcription factor binding  site of DNA damage  ribonucleoprotein complex  
Ontology : EGO-EBIhistone deacetylase complex  negative regulation of transcription by RNA polymerase II  kinetochore  nuclear chromosome, telomeric region  chromatin binding  protein binding  nucleus  nuclear envelope  nucleoplasm  nuclear heterochromatin  pericentric heterochromatin  nucleolus  cellular response to DNA damage stimulus  blood coagulation  chromocenter  viral process  PML body  transcriptional repressor complex  protein binding, bridging  nuclear pericentric heterochromatin  protein-containing complex  methylated histone binding  histone methyltransferase complex  identical protein binding  protein homodimerization activity  histone deacetylase binding  ribonucleoprotein complex binding  protein-containing complex binding  negative regulation of transcription, DNA-templated  negative regulation of transcription, DNA-templated  negative regulation of G0 to G1 transition  repressing transcription factor binding  site of DNA damage  ribonucleoprotein complex  
NDEx NetworkCBX5
Atlas of Cancer Signalling NetworkCBX5
Wikipedia pathwaysCBX5
Orthology - Evolution
OrthoDB23468
GeneTree (enSembl)ENSG00000094916
Phylogenetic Trees/Animal Genes : TreeFamCBX5
HOVERGENP45973
HOGENOMP45973
Homologs : HomoloGeneCBX5
Homology/Alignments : Family Browser (UCSC)CBX5
Gene fusions - Rearrangements
Fusion : MitelmanCBX5/NFE2 [12q13.13/12q13.13]  
Fusion : MitelmanPDIA4/CBX5 [7q36.1/12q13.13]  [t(7;12)(q36;q13)]  
Fusion PortalCBX5 12q13.13 NFE2 12q13.13 KIRC
Fusion PortalPDIA4 7q36.1 CBX5 12q13.13 PRAD
Fusion : QuiverCBX5
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCBX5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CBX5
dbVarCBX5
ClinVarCBX5
1000_GenomesCBX5 
Exome Variant ServerCBX5
ExAC (Exome Aggregation Consortium)ENSG00000094916
GNOMAD BrowserENSG00000094916
Varsome BrowserCBX5
Genetic variants : HAPMAP23468
Genomic Variants (DGV)CBX5 [DGVbeta]
DECIPHERCBX5 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCBX5 
Mutations
ICGC Data PortalCBX5 
TCGA Data PortalCBX5 
Broad Tumor PortalCBX5
OASIS PortalCBX5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCBX5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCBX5
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CBX5
DgiDB (Drug Gene Interaction Database)CBX5
DoCM (Curated mutations)CBX5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CBX5 (select a term)
intoGenCBX5
Cancer3DCBX5(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604478   
Orphanet
DisGeNETCBX5
MedgenCBX5
Genetic Testing Registry CBX5
NextProtP45973 [Medical]
TSGene23468
GENETestsCBX5
Target ValidationCBX5
Huge Navigator CBX5 [HugePedia]
snp3D : Map Gene to Disease23468
BioCentury BCIQCBX5
ClinGenCBX5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23468
Chemical/Pharm GKB GenePA26130
Clinical trialCBX5
Miscellaneous
canSAR (ICR)CBX5 (select the gene name)
Probes
Litterature
PubMed201 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCBX5
EVEXCBX5
GoPubMedCBX5
iHOPCBX5
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 6 10:55:59 CET 2018

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