Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

CDX1 (caudal type homeobox 1)

Identity

Alias_namescaudal type homeo box transcription factor 1
Other alias-
HGNC (Hugo) CDX1
LocusID (NCBI) 1044
Atlas_Id 43834
Location 5q32  [Link to chromosome band 5q32]
Location_base_pair Starts at 150166781 and ends at 150184558 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
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 Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  Esophagus: Barrett's esophagus, dysplasia and adenocarcinoma
Soft tissue tumors: an overview


External links

Nomenclature
HGNC (Hugo)CDX1   1805
Cards
Entrez_Gene (NCBI)CDX1  1044  caudal type homeobox 1
Aliases
GeneCards (Weizmann)CDX1
Ensembl hg19 (Hinxton)ENSG00000113722 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000113722 [Gene_View]  chr5:150166781-150184558 [Contig_View]  CDX1 [Vega]
ICGC DataPortalENSG00000113722
TCGA cBioPortalCDX1
AceView (NCBI)CDX1
Genatlas (Paris)CDX1
WikiGenes1044
SOURCE (Princeton)CDX1
Genetics Home Reference (NIH)CDX1
Genomic and cartography
GoldenPath hg38 (UCSC)CDX1  -     chr5:150166781-150184558 +  5q32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CDX1  -     5q32   [Description]    (hg19-Feb_2009)
EnsemblCDX1 - 5q32 [CytoView hg19]  CDX1 - 5q32 [CytoView hg38]
Mapping of homologs : NCBICDX1 [Mapview hg19]  CDX1 [Mapview hg38]
OMIM600746   
Gene and transcription
Genbank (Entrez)AF239666 BC096249 BC096250 BC096251 BC096252
RefSeq transcript (Entrez)NM_001804
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CDX1
Cluster EST : UnigeneHs.1545 [ NCBI ]
CGAP (NCI)Hs.1545
Alternative Splicing GalleryENSG00000113722
Gene ExpressionCDX1 [ NCBI-GEO ]   CDX1 [ EBI - ARRAY_EXPRESS ]   CDX1 [ SEEK ]   CDX1 [ MEM ]
Gene Expression Viewer (FireBrowse)CDX1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1044
GTEX Portal (Tissue expression)CDX1
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
Splice isoforms : SwissVarP47902
PhosPhoSitePlusP47902
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Caudal_activation_dom    Homeobox-like    Homeobox_CS    Homeobox_dom    Homeobox_metazoa    HTH_motif   
Domain families : Pfam (Sanger)Caudal_act (PF04731)    Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam04731    pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)CDX1
DMDM Disease mutations1044
Blocks (Seattle)CDX1
SuperfamilyP47902
Human Protein AtlasENSG00000113722
Peptide AtlasP47902
HPRD02849
IPIIPI00790637   IPI00784439   IPI00795021   IPI00607798   
Protein Interaction databases
DIP (DOE-UCLA)P47902
IntAct (EBI)P47902
FunCoupENSG00000113722
BioGRIDCDX1
STRING (EMBL)CDX1
ZODIACCDX1
Ontologies - Pathways
QuickGOP47902
Ontology : AmiGORNA polymerase II distal enhancer sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding  protein binding  nucleus  transcription from RNA polymerase II promoter  animal organ morphogenesis  anterior/posterior axis specification  regulation of somitogenesis  cell differentiation  transcription regulatory region DNA binding  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  bone morphogenesis  
Ontology : EGO-EBIRNA polymerase II distal enhancer sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding  protein binding  nucleus  transcription from RNA polymerase II promoter  animal organ morphogenesis  anterior/posterior axis specification  regulation of somitogenesis  cell differentiation  transcription regulatory region DNA binding  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  bone morphogenesis  
NDEx NetworkCDX1
Atlas of Cancer Signalling NetworkCDX1
Wikipedia pathwaysCDX1
Orthology - Evolution
OrthoDB1044
GeneTree (enSembl)ENSG00000113722
Phylogenetic Trees/Animal Genes : TreeFamCDX1
HOVERGENP47902
HOGENOMP47902
Homologs : HomoloGeneCDX1
Homology/Alignments : Family Browser (UCSC)CDX1
Gene fusions - Rearrangements
Fusion : MitelmanIRF2BP2/CDX1 [1q42.3/5q32]  [t(1;5)(q42;q32)]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCDX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CDX1
dbVarCDX1
ClinVarCDX1
1000_GenomesCDX1 
Exome Variant ServerCDX1
ExAC (Exome Aggregation Consortium)CDX1 (select the gene name)
Genetic variants : HAPMAP1044
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]  
Mutations and Diseases : HGMDCDX1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CDX1
DgiDB (Drug Gene Interaction Database)CDX1
DoCM (Curated mutations)CDX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CDX1 (select a term)
intoGenCDX1
Cancer3DCDX1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600746   
Orphanet
MedgenCDX1
Genetic Testing Registry CDX1
NextProtP47902 [Medical]
TSGene1044
GENETestsCDX1
Target ValidationCDX1
Huge Navigator CDX1 [HugePedia]
snp3D : Map Gene to Disease1044
BioCentury BCIQCDX1
ClinGenCDX1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1044
Chemical/Pharm GKB GenePA26351
Clinical trialCDX1
Miscellaneous
canSAR (ICR)CDX1 (select the gene name)
Probes
Litterature
PubMed42 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCDX1
EVEXCDX1
GoPubMedCDX1
iHOPCDX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Jun 7 12:27:53 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.