CDX1 (caudal type homeobox 1)

Gene

• Entrez ID: 1044
• Gene name: Caudal type homeobox 1
• Gene symbol: CDX1
• Synonyms (NCBI Gene): -
• Chromosome: 5
• Chromosome location: 5q32
• Summary: This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal al

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT054157	hsa-miR-296-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, qRT-PCR, Western blot	23353818
MIRT054157	hsa-miR-296-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, qRT-PCR, Western blot	23353818
MIRT054157	hsa-miR-296-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, qRT-PCR, Western blot	23353818
MIRT054157	hsa-miR-296-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, qRT-PCR, Western blot	23353818
MIRT447995	hsa-miR-4282	PAR-CLIP	22100165
MIRT447996	hsa-miR-4635	PAR-CLIP	22100165
MIRT447994	hsa-miR-3928-5p	PAR-CLIP	22100165
MIRT447993	hsa-miR-6806-3p	PAR-CLIP	22100165
MIRT447992	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT447991	hsa-miR-7843-3p	PAR-CLIP	22100165
MIRT447990	hsa-miR-127-5p	PAR-CLIP	22100165
MIRT447995	hsa-miR-4282	PAR-CLIP	22100165
MIRT447996	hsa-miR-4635	PAR-CLIP	22100165
MIRT447994	hsa-miR-3928-5p	PAR-CLIP	22100165
MIRT447993	hsa-miR-6806-3p	PAR-CLIP	22100165
MIRT447992	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT447991	hsa-miR-7843-3p	PAR-CLIP	22100165
MIRT447990	hsa-miR-127-5p	PAR-CLIP	22100165
MIRT882812	hsa-miR-493	CLIP-seq
MIRT882813	hsa-miR-943	CLIP-seq
MIRT1961709	hsa-miR-4281	CLIP-seq
MIRT1961710	hsa-miR-4286	CLIP-seq
MIRT2198327	hsa-miR-3130-5p	CLIP-seq
MIRT2198328	hsa-miR-4482	CLIP-seq
MIRT2446774	hsa-miR-1913	CLIP-seq
MIRT2446775	hsa-miR-1915	CLIP-seq
MIRT2446776	hsa-miR-3127-3p	CLIP-seq
MIRT2446777	hsa-miR-3130-3p	CLIP-seq
MIRT2446778	hsa-miR-324-3p	CLIP-seq
MIRT2446779	hsa-miR-4267	CLIP-seq
MIRT2446780	hsa-miR-4279	CLIP-seq
MIRT1961710	hsa-miR-4286	CLIP-seq
MIRT2446781	hsa-miR-4313	CLIP-seq
MIRT2446782	hsa-miR-4685-5p	CLIP-seq
MIRT2446783	hsa-miR-4726-3p	CLIP-seq
MIRT2446784	hsa-miR-4768-5p	CLIP-seq
MIRT2446785	hsa-miR-766	CLIP-seq
MIRT2446786	hsa-miR-942	CLIP-seq
MIRT2446777	hsa-miR-3130-3p	CLIP-seq
MIRT2446779	hsa-miR-4267	CLIP-seq
MIRT1961710	hsa-miR-4286	CLIP-seq
MIRT2446785	hsa-miR-766	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription cis-regulatory region binding	IDA	24623306
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	15774940
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	15774940
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IBA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005515	Function	Protein binding	IPI	19059241
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0007389	Process	Pattern specification process	IEA
GO:0008327	Function	Methyl-CpG binding	IDA	28473536
GO:0009880	Process	Embryonic pattern specification	IBA
GO:0009887	Process	Animal organ morphogenesis	TAS	8530027
GO:0009948	Process	Anterior/posterior axis specification	IBA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0014807	Process	Regulation of somitogenesis	IEA
GO:0014807	Process	Regulation of somitogenesis	ISS
GO:0030154	Process	Cell differentiation	IBA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	15774940
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	24623306
GO:0048565	Process	Digestive tract development	IBA
GO:0060349	Process	Bone morphogenesis	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 600746
• HGNC: 1805
• e!Ensembl: ENSG00000113722

Protein

• UniProt ID: P47902
• Protein name: Homeobox protein CDX-1 (Caudal-type homeobox protein 1)
• Protein function: Plays a role in transcriptional regulation (PubMed:24623306). Involved in activated KRAS-mediated transcriptional activation of PRKD1 in colorectal cancer (CRC) cells (PubMed:24623306). Binds to the PRKD1 promoter in colorectal cancer (CRC) cell
• PDB: 5LUX, 7Q3O
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04731	Caudal_act	13 → 146	Caudal like protein activation region	Family
  PF00046	Homeodomain	155 → 211	Homeodomain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Intestinal epithelium.
• Sequence:

  MYVGYVLDKDSPVYPGPARPASLGLGPQAYGPPAPPPAPPQYPDFSSYSHVEPAPAPPTA
  WGAPFPAPKDDWAAAYGPGPAAPAASPASLAFGPPPDFSPVPAPPGPGPGLLAQPLGGPG
  TPSSPGAQRPTPYEWMRRSVAAGGGGGSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYIT
  IRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQPPQPPMAHDITATPAGPSL
  GGLCPSNTSLLATSSPMPVKEEFLP

• Sequence length: 265

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CDX1-related disorder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RECTUM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	15910596, 9247467		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of colon	Adenocarcinoma Of Colon	BEFREE	12270138, 9396760		★☆☆☆☆ Found in Text Mining only
Arnold-Chiari Malformation, Type I	Arnold-Chiari malformation	BEFREE	23437350		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	28149331	Associate	★☆☆☆☆ Found in Text Mining only
Barrett Epithelium	Barrett Epithelium	BEFREE	12560917		★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Barrett esophagus	BEFREE	15894614, 18953412, 19468668, 21075347, 23687410, 23918153, 24713057		★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Barrett esophagus	Pubtator	15894614, 18953412, 19468668, 22016432, 23687410, 23918153, 35437997	Associate	★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Barrett esophagus	LHGDN	18953412		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	22749770, 30289576	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	12970739, 15378566, 9247467		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	28418032	Associate	★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	31841177		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	31841177		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	BEFREE	31523056		★☆☆☆☆ Found in Text Mining only
Chondrosarcoma Mesenchymal	Chondrosarcoma	Pubtator	23185413, 37905608	Associate	★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	10833444, 12124393, 12970739, 14508520, 15215241, 23624503		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic Neoplasms	LHGDN	15215241, 18187048		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic Neoplasms	BEFREE	25939752		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	10833444, 12124393, 12970739, 14704280, 15378566, 15526363, 16596323, 19188603, 21393996, 22349300, 23618814, 26537799, 28226180, 9593754		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	11566252, 18819935, 19188603, 21368208, 21393996, 22719836, 25775580, 26537799, 30909444, 35715570, 36224588, 36902272, 38216091, 9593754	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	LHGDN	12124393, 12970739		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	16491830	Inhibit	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	BEFREE	9593754		★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	24839999		★☆☆☆☆ Found in Text Mining only
Dermatitis Atopic	Atopic dermatitis	Pubtator	28149331	Associate	★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	BEFREE	21613300		★☆☆☆☆ Found in Text Mining only
Enterocolitis	Enterocolitis	BEFREE	11566252		★☆☆☆☆ Found in Text Mining only
Enterocolitis	Enterocolitis	Pubtator	11566252	Inhibit	★☆☆☆☆ Found in Text Mining only
Eosinophilic Esophagitis	Eosinophilia	Pubtator	35437997	Stimulate	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	26683359	Associate	★☆☆☆☆ Found in Text Mining only
Esophagitis	Esotropia	Pubtator	23687410	Inhibit	★☆☆☆☆ Found in Text Mining only
Gastritis	Gastritis	BEFREE	11846061, 18775915, 22749770		★☆☆☆☆ Found in Text Mining only
Gastritis	Gastritis	Pubtator	22749770	Associate	★☆☆☆☆ Found in Text Mining only
Gastritis, Atrophic	Gastritis	LHGDN	11846061		★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	BEFREE	23918153		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	11566252		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung disease	Pubtator	11566252	Inhibit	★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	21368208	Associate	★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal disease	Pubtator	14525978, 21532856, 22749770	Associate	★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal disease	Pubtator	30289576	Stimulate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	17855634		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	27566019		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of gastrointestinal tract	Malignant gastrointestinal tract tumors	BEFREE	22901255		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	15753353		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	14615935, 21532856, 23353818, 24078401, 30289576		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	14508520, 19188603, 21532856, 26537799, 30685841, 31416838, 9593754		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	31841177		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	10833444, 12124393, 12970739, 14508520, 15215241, 23624503		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	15526363	Associate	★☆☆☆☆ Found in Text Mining only
Mesenchymal Chondrosarcoma	Mesenchymal Chondrosarcoma	BEFREE	23185413		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21393996, 23185413, 23613102, 23618814, 23624503, 24839999, 25320087, 25939752, 27566019, 9593754, 9926923		★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	15526363		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	15753353		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	28418924	Associate	★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Retinoblastoma	BEFREE	14508520		★☆☆☆☆ Found in Text Mining only
Rhinitis Allergic	Rhinitis	Pubtator	28149331	Associate	★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	29104083	Associate	★☆☆☆☆ Found in Text Mining only
Spondylocostal dysostosis autosomal recessive	Spondylocostal dysostosis	Pubtator	22215184	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	31523056		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	21532856, 23353818, 24078401, 30289576		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	14525978, 14615935, 21532856, 30289576, 30685841, 31868807, 34312322	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	22749770	Inhibit	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	31841177	Associate	★☆☆☆☆ Found in Text Mining only