HOXD9 (homeobox D9)

Gene

• Entrez ID: 3235
• Gene name: Homeobox D9
• Gene symbol: HOXD9
• Synonyms (NCBI Gene): HOX4, HOX4C, Hox-4.3, Hox-5.2
• Chromosome: 2
• Chromosome location: 2q31.1
• Summary: This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene cluster

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT724683	hsa-miR-3614-5p	HITS-CLIP	19536157
MIRT724682	hsa-miR-29b-2-5p	HITS-CLIP	19536157
MIRT715096	hsa-miR-3156-5p	HITS-CLIP	19536157
MIRT715095	hsa-miR-361-3p	HITS-CLIP	19536157
MIRT715094	hsa-miR-6728-3p	HITS-CLIP	19536157
MIRT715093	hsa-miR-4769-3p	HITS-CLIP	19536157
MIRT715092	hsa-miR-6817-5p	HITS-CLIP	19536157
MIRT715091	hsa-miR-4713-3p	HITS-CLIP	19536157
MIRT715090	hsa-miR-4727-5p	HITS-CLIP	19536157
MIRT715089	hsa-miR-4715-3p	HITS-CLIP	19536157
MIRT536752	hsa-miR-6776-3p	PAR-CLIP	22012620
MIRT536751	hsa-miR-488-5p	PAR-CLIP	22012620
MIRT536750	hsa-miR-454-5p	PAR-CLIP	22012620
MIRT536749	hsa-miR-2355-5p	PAR-CLIP	22012620
MIRT442589	hsa-miR-551b-5p	PAR-CLIP	22100165
MIRT442588	hsa-miR-4786-3p	PAR-CLIP	22100165
MIRT442587	hsa-miR-625-5p	PAR-CLIP	22100165
MIRT442586	hsa-miR-6795-5p	PAR-CLIP	22100165
MIRT442585	hsa-miR-6887-5p	PAR-CLIP	22100165
MIRT442584	hsa-miR-328-5p	PAR-CLIP	22100165
MIRT442583	hsa-miR-6885-5p	PAR-CLIP	22100165
MIRT442582	hsa-miR-1275	PAR-CLIP	22100165
MIRT442581	hsa-miR-4665-5p	PAR-CLIP	22100165
MIRT442579	hsa-miR-7109-5p	PAR-CLIP	22100165
MIRT442580	hsa-miR-6751-5p	PAR-CLIP	22100165
MIRT442578	hsa-miR-6803-5p	PAR-CLIP	22100165
MIRT442577	hsa-miR-450a-2-3p	PAR-CLIP	22100165
MIRT442576	hsa-miR-4260	PAR-CLIP	22100165
MIRT442575	hsa-miR-5572	PAR-CLIP	22100165
MIRT442589	hsa-miR-551b-5p	PAR-CLIP	22100165
MIRT442588	hsa-miR-4786-3p	PAR-CLIP	22100165
MIRT442587	hsa-miR-625-5p	PAR-CLIP	22100165
MIRT442586	hsa-miR-6795-5p	PAR-CLIP	22100165
MIRT442585	hsa-miR-6887-5p	PAR-CLIP	22100165
MIRT442584	hsa-miR-328-5p	PAR-CLIP	22100165
MIRT442583	hsa-miR-6885-5p	PAR-CLIP	22100165
MIRT442582	hsa-miR-1275	PAR-CLIP	22100165
MIRT442581	hsa-miR-4665-5p	PAR-CLIP	22100165
MIRT442579	hsa-miR-7109-5p	PAR-CLIP	22100165
MIRT442580	hsa-miR-6751-5p	PAR-CLIP	22100165
MIRT442578	hsa-miR-6803-5p	PAR-CLIP	22100165
MIRT442577	hsa-miR-450a-2-3p	PAR-CLIP	22100165
MIRT442576	hsa-miR-4260	PAR-CLIP	22100165
MIRT442575	hsa-miR-5572	PAR-CLIP	22100165
MIRT724683	hsa-miR-3614-5p	HITS-CLIP	19536157
MIRT724682	hsa-miR-29b-2-5p	HITS-CLIP	19536157
MIRT715096	hsa-miR-3156-5p	HITS-CLIP	19536157
MIRT715095	hsa-miR-361-3p	HITS-CLIP	19536157
MIRT715094	hsa-miR-6728-3p	HITS-CLIP	19536157
MIRT715093	hsa-miR-4769-3p	HITS-CLIP	19536157
MIRT715092	hsa-miR-6817-5p	HITS-CLIP	19536157
MIRT715091	hsa-miR-4713-3p	HITS-CLIP	19536157
MIRT715090	hsa-miR-4727-5p	HITS-CLIP	19536157
MIRT715089	hsa-miR-4715-3p	HITS-CLIP	19536157
MIRT536752	hsa-miR-6776-3p	PAR-CLIP	22012620
MIRT536751	hsa-miR-488-5p	PAR-CLIP	22012620
MIRT536750	hsa-miR-454-5p	PAR-CLIP	22012620
MIRT536749	hsa-miR-2355-5p	PAR-CLIP	22012620
MIRT442589	hsa-miR-551b-5p	PAR-CLIP	22100165
MIRT442588	hsa-miR-4786-3p	PAR-CLIP	22100165
MIRT442587	hsa-miR-625-5p	PAR-CLIP	22100165
MIRT442586	hsa-miR-6795-5p	PAR-CLIP	22100165
MIRT442585	hsa-miR-6887-5p	PAR-CLIP	22100165
MIRT442584	hsa-miR-328-5p	PAR-CLIP	22100165
MIRT442583	hsa-miR-6885-5p	PAR-CLIP	22100165
MIRT442582	hsa-miR-1275	PAR-CLIP	22100165
MIRT442581	hsa-miR-4665-5p	PAR-CLIP	22100165
MIRT442579	hsa-miR-7109-5p	PAR-CLIP	22100165
MIRT442580	hsa-miR-6751-5p	PAR-CLIP	22100165
MIRT442578	hsa-miR-6803-5p	PAR-CLIP	22100165
MIRT442577	hsa-miR-450a-2-3p	PAR-CLIP	22100165
MIRT442576	hsa-miR-4260	PAR-CLIP	22100165
MIRT442575	hsa-miR-5572	PAR-CLIP	22100165
MIRT442589	hsa-miR-551b-5p	PAR-CLIP	22100165
MIRT442588	hsa-miR-4786-3p	PAR-CLIP	22100165
MIRT442587	hsa-miR-625-5p	PAR-CLIP	22100165
MIRT442586	hsa-miR-6795-5p	PAR-CLIP	22100165
MIRT442585	hsa-miR-6887-5p	PAR-CLIP	22100165
MIRT442584	hsa-miR-328-5p	PAR-CLIP	22100165
MIRT442583	hsa-miR-6885-5p	PAR-CLIP	22100165
MIRT442582	hsa-miR-1275	PAR-CLIP	22100165
MIRT442581	hsa-miR-4665-5p	PAR-CLIP	22100165
MIRT442579	hsa-miR-7109-5p	PAR-CLIP	22100165
MIRT442580	hsa-miR-6751-5p	PAR-CLIP	22100165
MIRT442578	hsa-miR-6803-5p	PAR-CLIP	22100165
MIRT442577	hsa-miR-450a-2-3p	PAR-CLIP	22100165
MIRT442576	hsa-miR-4260	PAR-CLIP	22100165
MIRT442575	hsa-miR-5572	PAR-CLIP	22100165
MIRT1053812	hsa-miR-3120-3p	CLIP-seq
MIRT1053813	hsa-miR-570	CLIP-seq
MIRT2244601	hsa-miR-1224-5p	CLIP-seq
MIRT1053812	hsa-miR-3120-3p	CLIP-seq
MIRT2244602	hsa-miR-4751	CLIP-seq
MIRT1053813	hsa-miR-570	CLIP-seq
MIRT2547485	hsa-miR-3141	CLIP-seq
MIRT2547486	hsa-miR-3914	CLIP-seq
MIRT2547487	hsa-miR-4311	CLIP-seq
MIRT2547488	hsa-miR-4419a	CLIP-seq
MIRT2547489	hsa-miR-4477b	CLIP-seq
MIRT2547490	hsa-miR-4481	CLIP-seq
MIRT2547491	hsa-miR-4510	CLIP-seq
MIRT2547492	hsa-miR-4654	CLIP-seq
MIRT2547493	hsa-miR-4719	CLIP-seq
MIRT2547494	hsa-miR-4745-5p	CLIP-seq
MIRT2547495	hsa-miR-4769-5p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HOXD9	Activation	7926763

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	1756725
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	1756725
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
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:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	1756725
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:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0006351	Process	DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007338	Process	Single fertilization	IEA
GO:0007519	Process	Skeletal muscle tissue development	IEA
GO:0008344	Process	Adult locomotory behavior	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IBA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0009954	Process	Proximal/distal pattern formation	IBA
GO:0009954	Process	Proximal/distal pattern formation	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0030879	Process	Mammary gland development	IEA
GO:0035115	Process	Embryonic forelimb morphogenesis	IEA
GO:0035136	Process	Forelimb morphogenesis	IEA
GO:0035137	Process	Hindlimb morphogenesis	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048704	Process	Embryonic skeletal system morphogenesis	IBA
GO:0048704	Process	Embryonic skeletal system morphogenesis	IEA
GO:0048706	Process	Embryonic skeletal system development	IEA
GO:0048935	Process	Peripheral nervous system neuron development	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

Other IDs

• MIM: 142982
• HGNC: 5140
• e!Ensembl: ENSG00000128709

Protein

• UniProt ID: P28356
• Protein name: Homeobox protein Hox-D9 (Homeobox protein Hox-4C) (Homeobox protein Hox-5.2)
• Protein function: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04617	Hox9_act	11 → 133		Family
  PF00046	Homeodomain	286 → 342	Homeodomain	Domain

• Sequence:

  MLGGSAGRLKMSSSGTLSNYYVDSLIGHEGDEVFAARFGPPGPGAQGRPAGVADGPAATA
  AEFASCSFAPRSAVFSASWSAVPSQPPAAAAMSGLYHPYVPPPPLAASASEPGRYVRSWM
  EPLPGFPGGAGGGGGGGGGGPGRGPSPGPSGPANGRHYGIKPETRAAPAPATAASTTSSS
  STSLSSSSKRTECSVARESQGSSGPEFSCNSFLQEKAAAATGGTGPGAGIGAATGTGGSS
  EPSACSDHPIPGCSLKEEEKQHSQPQQQQLDPNNPAANWIHARSTRKKRCPYTKYQTLEL
  EKEFLFNMYLTRDRRYEVARILNLTERQVKIWFQNRRMKMKKMSKEKCPKGD

• Sequence length: 352

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
CARCINOMA, HEPATOCELLULAR	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HOXD9-related disorder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Astrocytoma	Astrocytoma	BEFREE	21600039		★☆☆☆☆ Found in Text Mining only
Astrocytoma	Astrocytoma	Pubtator	21600039	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	33428601, 34452548	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	30247807, 34116652, 34911488, 35030478, 36397165	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	26391404	Associate	★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	31477279		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	31477279		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	BEFREE	24089088, 30832707		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	24089088, 30832707	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	CTD_human_DG	26075790		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	BEFREE	26075790		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Neoplasms	Colorectal Neoplasms	CTD_human_DG	26075790		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	26075790	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital contractural arachnodactyly	Congenital Contractural Arachnodactyly	BEFREE	30832707		★☆☆☆☆ Found in Text Mining only
Congenital Dysplasia Of The Hip	Developmental dysplasia of the hip	BEFREE	22520331		★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	11352232, 9324017		★☆☆☆☆ Found in Text Mining only
Developmental Dysplasia of the Hip	Developmental dysplasia of the hip	Pubtator	22520331	Associate	★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	39511608	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	15770739	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	15770739	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	21600039		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	21600039, 40209540	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	21600039, 31680311		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	21600039, 37603105	Associate	★☆☆☆☆ Found in Text Mining only
LEUKOENCEPHALOPATHY, BRAIN CALCIFICATIONS, AND CYSTS	LEUKOENCEPHALOPATHY, BRAIN CALCIFICATIONS, AND CYSTS	BEFREE	27301951		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	26514226, 27301951		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CTD_human_DG	28284560		★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	24014427	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	CTD_human_DG	26075790		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	31547840		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21600039, 26514226, 31746370		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	31477279		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	24014427	Associate	★☆☆☆☆ Found in Text Mining only
Microvascular Angina	Microvascular angina	Pubtator	34911488	Stimulate	★☆☆☆☆ Found in Text Mining only
Mucinous Adenocarcinoma	Mucinous Adenocarcinoma	CTD_human_DG	26075790		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26075790, 31477279		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	7501971		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	7501971	Associate	★☆☆☆☆ Found in Text Mining only
Ovarian Diseases	Ovarian diseases	Pubtator	26075790	Associate	★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	CTD_human_DG	26075790		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	36213580	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	34558641	Associate	★☆☆☆☆ Found in Text Mining only
Refractory anemias	Anemia	BEFREE	7501971		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	11352232, 7501971, 9324017		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	LHGDN	12060849		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	LHGDN	15770739		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	31547840		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37225681	Associate	★☆☆☆☆ Found in Text Mining only
Syndactyly, type 2	Syndactyly	BEFREE	11778160		★☆☆☆☆ Found in Text Mining only
Thymic Carcinoma	Thymic Carcinoma	BEFREE	31746370		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	33428601	Associate	★☆☆☆☆ Found in Text Mining only