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CDX1 (caudal type homeobox 1)

Identity

Alias (NCBI)-
HGNC (Hugo) CDX1
HGNC Previous namecaudal type homeo box transcription factor 1
LocusID (NCBI) 1044
Atlas_Id 43834
Location 5q32  [Link to chromosome band 5q32]
Location_base_pair Starts at 150166778 and ends at 150184558 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)
IRF2BP2 (1q42.3) / CDX1 (5q32)IRF2BP2 1q42.3 / CDX1 5q32

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 Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(1;5)(q21;q32) PDE4DIP/PDGFRB::t(1;5)(q21-23;q32) TPM3/PDGFRB::t(1;5)(q21-23;q31-33)


External links

 

Nomenclature
HGNC (Hugo)CDX1   1805
Cards
Entrez_Gene (NCBI)CDX1    caudal type homeobox 1
Aliases
GeneCards (Weizmann)CDX1
Ensembl hg19 (Hinxton)ENSG00000113722 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000113722 [Gene_View]  ENSG00000113722 [Sequence]  chr5:150166778-150184558 [Contig_View]  CDX1 [Vega]
ICGC DataPortalENSG00000113722
TCGA cBioPortalCDX1
AceView (NCBI)CDX1
Genatlas (Paris)CDX1
SOURCE (Princeton)CDX1
Genetics Home Reference (NIH)CDX1
Genomic and cartography
GoldenPath hg38 (UCSC)CDX1  -     chr5:150166778-150184558 +  5q32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CDX1  -     5q32   [Description]    (hg19-Feb_2009)
GoldenPathCDX1 - 5q32 [CytoView hg19]  CDX1 - 5q32 [CytoView hg38]
ImmunoBaseENSG00000113722
Genome Data Viewer NCBICDX1 [Mapview hg19]  
OMIM600746   
Gene and transcription
Genbank (Entrez)AF239666 BC096249 BC096250 BC096251 BC096252
RefSeq transcript (Entrez)NM_001804
Consensus coding sequences : CCDS (NCBI)CDX1
Gene ExpressionCDX1 [ NCBI-GEO ]   CDX1 [ EBI - ARRAY_EXPRESS ]   CDX1 [ SEEK ]   CDX1 [ MEM ]
Gene Expression Viewer (FireBrowse)CDX1 [ Firebrowse - Broad ]
GenevisibleExpression of CDX1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1044
GTEX Portal (Tissue expression)CDX1
Human Protein AtlasENSG00000113722-CDX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP47902   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP47902  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP47902
PhosPhoSitePlusP47902
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Caudal_activation_dom    Homeobox-like_sf    Homeobox_CS    Homeobox_dom    Homeobox_metazoa    HTH_motif   
Domain families : Pfam (Sanger)Caudal_act (PF04731)    Homeodomain (PF00046)   
Domain families : Pfam (NCBI)pfam04731    pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)CDX1
PDB (RSDB)5LUX   
PDB Europe5LUX   
PDB (PDBSum)5LUX   
PDB (IMB)5LUX   
Structural Biology KnowledgeBase5LUX   
SCOP (Structural Classification of Proteins)5LUX   
CATH (Classification of proteins structures)5LUX   
SuperfamilyP47902
AlphaFold pdb e-kbP47902   
Human Protein Atlas [tissue]ENSG00000113722-CDX1 [tissue]
HPRD02849
Protein Interaction databases
DIP (DOE-UCLA)P47902
IntAct (EBI)P47902
BioGRIDCDX1
STRING (EMBL)CDX1
ZODIACCDX1
Ontologies - Pathways
QuickGOP47902
Ontology : AmiGOchromatin  transcription cis-regulatory region binding  RNA polymerase II transcription regulatory region sequence-specific DNA binding  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription activator activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  regulation of transcription by RNA polymerase II  methyl-CpG binding  embryo development  animal organ morphogenesis  anterior/posterior axis specification  regulation of somitogenesis  cell differentiation  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  bone morphogenesis  sequence-specific double-stranded DNA binding  
Ontology : EGO-EBIchromatin  transcription cis-regulatory region binding  RNA polymerase II transcription regulatory region sequence-specific DNA binding  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription activator activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  regulation of transcription by RNA polymerase II  methyl-CpG binding  embryo development  animal organ morphogenesis  anterior/posterior axis specification  regulation of somitogenesis  cell differentiation  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  bone morphogenesis  sequence-specific double-stranded DNA binding  
NDEx NetworkCDX1
Atlas of Cancer Signalling NetworkCDX1
Wikipedia pathwaysCDX1
Orthology - Evolution
OrthoDB1044
GeneTree (enSembl)ENSG00000113722
Phylogenetic Trees/Animal Genes : TreeFamCDX1
Homologs : HomoloGeneCDX1
Homology/Alignments : Family Browser (UCSC)CDX1
Gene fusions - Rearrangements
Fusion : MitelmanIRF2BP2/CDX1 [1q42.3/5q32]  
Fusion : QuiverCDX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCDX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CDX1
dbVarCDX1
ClinVarCDX1
MonarchCDX1
1000_GenomesCDX1 
Exome Variant ServerCDX1
GNOMAD BrowserENSG00000113722
Varsome BrowserCDX1
ACMGCDX1 variants
VarityP47902
Genomic Variants (DGV)CDX1 [DGVbeta]
DECIPHERCDX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCDX1 
Mutations
ICGC Data PortalCDX1 
TCGA Data PortalCDX1 
Broad Tumor PortalCDX1
OASIS PortalCDX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCDX1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DCDX1
Mutations and Diseases : HGMDCDX1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaCDX1
DgiDB (Drug Gene Interaction Database)CDX1
DoCM (Curated mutations)CDX1
CIViC (Clinical Interpretations of Variants in Cancer)CDX1
Cancer3DCDX1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600746   
Orphanet
DisGeNETCDX1
MedgenCDX1
Genetic Testing Registry CDX1
NextProtP47902 [Medical]
GENETestsCDX1
Target ValidationCDX1
Huge Navigator CDX1 [HugePedia]
ClinGenCDX1
Clinical trials, drugs, therapy
MyCancerGenomeCDX1
Protein Interactions : CTDCDX1
Pharm GKB GenePA26351
PharosP47902
Clinical trialCDX1
Miscellaneous
canSAR (ICR)CDX1
HarmonizomeCDX1
DataMed IndexCDX1
Probes
Litterature
PubMed54 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXCDX1
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 15:03:24 CEST 2021

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