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	Relationship Type	References	Evidence Score
Anorectal Malformations	Associate	34671974	★☆☆☆☆ Found in Text Mining only
Arnold Chiari Malformation	Associate	23437350	★☆☆☆☆ Found in Text Mining only
Asthma	Associate	28149331	★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Associate	15894614, 18953412, 19468668, 22016432, 23687410, 23918153, 35437997	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	22749770, 30289576	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	28418032	★☆☆☆☆ Found in Text Mining only
Chondrosarcoma Mesenchymal	Associate	23185413, 37905608	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	11566252, 18819935, 19188603, 21368208, 21393996, 22719836, 25775580, 26537799, 30909444, 35715570, 36224588, 36902272, 38216091, 9593754	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Inhibit	16491830	★☆☆☆☆ Found in Text Mining only
Dermatitis Atopic	Associate	28149331	★☆☆☆☆ Found in Text Mining only
Enterocolitis	Inhibit	11566252	★☆☆☆☆ Found in Text Mining only
Eosinophilic Esophagitis	Stimulate	35437997	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Associate	26683359	★☆☆☆☆ Found in Text Mining only
Esophagitis	Inhibit	23687410	★☆☆☆☆ Found in Text Mining only
Gastritis	Associate	22749770	★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Inhibit	11566252	★☆☆☆☆ Found in Text Mining only
Hypoxia	Associate	21368208	★☆☆☆☆ Found in Text Mining only
Inflammation	Stimulate	15894614	★☆☆☆☆ Found in Text Mining only
Inflammation	Associate	22749770	★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Associate	14525978, 21532856, 22749770	★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Stimulate	30289576	★☆☆☆☆ Found in Text Mining only
Melanoma	Associate	15526363	★☆☆☆☆ Found in Text Mining only
Metaplasia	Associate	22749770	★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	36224588	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	17236756, 19059241, 22749770, 24839999, 30685841, 30909444, 37905608	★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	21393996, 38216091, 9593754	★☆☆☆☆ Found in Text Mining only
Neoplasms	Stimulate	21532856, 28418924	★☆☆☆☆ Found in Text Mining only
Neuhauser syndrome	Associate	34312322	★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Associate	28418924	★☆☆☆☆ Found in Text Mining only
Polyps	Inhibit	33525395	★☆☆☆☆ Found in Text Mining only
Retinal Dysplasia	Stimulate	21532856	★☆☆☆☆ Found in Text Mining only
Retinal Dysplasia	Associate	9593754	★☆☆☆☆ Found in Text Mining only
Rhinitis Allergic	Associate	28149331	★☆☆☆☆ Found in Text Mining only
Sarcoma	Associate	29104083	★☆☆☆☆ Found in Text Mining only
Spondylocostal dysostosis autosomal recessive	Associate	22215184	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	14525978, 14615935, 21532856, 30289576, 30685841, 31868807, 34312322	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Inhibit	22749770	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Associate	31841177	★☆☆☆☆ Found in Text Mining only