HOXA4 (homeobox A4)

Gene

• Entrez ID: 3201
• Gene name: Homeobox A4
• Gene symbol: HOXA4
• Synonyms (NCBI Gene): HOX1, HOX1D
• Chromosome: 7
• Chromosome location: 7p15.2
• Summary: In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic develo

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1053158	hsa-miR-1253	CLIP-seq
MIRT1053159	hsa-miR-1255a	CLIP-seq
MIRT1053160	hsa-miR-1255b	CLIP-seq
MIRT1053161	hsa-miR-1275	CLIP-seq
MIRT1053162	hsa-miR-1294	CLIP-seq
MIRT1053163	hsa-miR-22	CLIP-seq
MIRT1053164	hsa-miR-300	CLIP-seq
MIRT1053165	hsa-miR-3160-3p	CLIP-seq
MIRT1053166	hsa-miR-3165	CLIP-seq
MIRT1053167	hsa-miR-3618	CLIP-seq
MIRT1053168	hsa-miR-3653	CLIP-seq
MIRT1053169	hsa-miR-3658	CLIP-seq
MIRT1053170	hsa-miR-3691-5p	CLIP-seq
MIRT1053171	hsa-miR-381	CLIP-seq
MIRT1053172	hsa-miR-3915	CLIP-seq
MIRT1053173	hsa-miR-3928	CLIP-seq
MIRT1053174	hsa-miR-4271	CLIP-seq
MIRT1053175	hsa-miR-4316	CLIP-seq
MIRT1053176	hsa-miR-4434	CLIP-seq
MIRT1053177	hsa-miR-4453	CLIP-seq
MIRT1053178	hsa-miR-4475	CLIP-seq
MIRT1053179	hsa-miR-4487	CLIP-seq
MIRT1053180	hsa-miR-4506	CLIP-seq
MIRT1053181	hsa-miR-4516	CLIP-seq
MIRT1053182	hsa-miR-4525	CLIP-seq
MIRT1053183	hsa-miR-4538	CLIP-seq
MIRT1053184	hsa-miR-4643	CLIP-seq
MIRT1053185	hsa-miR-4651	CLIP-seq
MIRT1053186	hsa-miR-466	CLIP-seq
MIRT1053187	hsa-miR-4665-5p	CLIP-seq
MIRT1053188	hsa-miR-4722-5p	CLIP-seq
MIRT1053189	hsa-miR-4723-5p	CLIP-seq
MIRT1053190	hsa-miR-4725-3p	CLIP-seq
MIRT1053191	hsa-miR-4729	CLIP-seq
MIRT1053192	hsa-miR-4761-5p	CLIP-seq
MIRT1053193	hsa-miR-4768-3p	CLIP-seq
MIRT1053194	hsa-miR-4789-3p	CLIP-seq
MIRT1053195	hsa-miR-556-5p	CLIP-seq
MIRT1053196	hsa-miR-558	CLIP-seq
MIRT1053197	hsa-miR-581	CLIP-seq
MIRT1053198	hsa-miR-608	CLIP-seq
MIRT1053199	hsa-miR-625	CLIP-seq
MIRT1053200	hsa-miR-935	CLIP-seq
MIRT2547322	hsa-miR-4778-3p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
TFAP2A	Repression	8759021

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
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	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:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IBA
GO:0005654	Component	Nucleoplasm	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0009653	Process	Anatomical structure morphogenesis	TAS	1675427
GO:0009952	Process	Anterior/posterior pattern specification	IBA
GO:0016604	Component	Nuclear body	IDA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0048704	Process	Embryonic skeletal system morphogenesis	IBA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 142953
• HGNC: 5105
• e!Ensembl: ENSG00000197576

Protein

• UniProt ID: Q00056
• Protein name: Homeobox protein Hox-A4 (Homeobox protein Hox-1.4) (Homeobox protein Hox-1D)
• 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. Binds to sites in the 5'-flanking sequence of its coding region wit
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00046	Homeodomain	216 → 272	Homeodomain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Embryonic nervous system.
• Sequence:

  MTMSSFLINSNYIEPKFPPFEEYAQHSGSGGADGGPGGGPGYQQPPAPPTQHLPLQQPQL
  PHAGGGREPTASYYAPRTAREPAYPAAALYPAHGAADTAYPYGYRGGASPGRPPQPEQPP
  AQAKGPAHGLHASHVLQPQLPPPLQPRAVPPAAPRRCEAAPATPGVPAGGSAPACPLLLA
  DKSPLGLKGKEPVVYPWMKKIHVSAVNPSYNGGEPKRSRTAYTRQQVLELEKEFHFNRYL
  TRRRRIEIAHTLCLSERQVKIWFQNRRMKWKKDHKLPNTKMRSSNSASASAGPPGKAQTQ
  SPHLHPHPHPSTSTPVPSSI

• Sequence length: 320

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
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HOXA4-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOSPADIAS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute monocytic leukemia	Monocytic Leukemia	BEFREE	19563517		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma	Adenocarcinoma	BEFREE	19281776		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	30501603		★☆☆☆☆ Found in Text Mining only
Blast Phase	Blast phase chronic myelogenous leukemia	BEFREE	17785556		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	30203578		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	16127744, 23980595	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	23980595		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	29700285		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	32444962	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	19281776, 29700285		★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	LHGDN	16688227		★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	BEFREE	17203192, 17254481		★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	16127744	Inhibit	★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	28464221		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	23980595	Stimulate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	23980595, 28464221, 29700285, 30552679		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	16127744	Inhibit	★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	25585874		★☆☆☆☆ Found in Text Mining only
Epithelial ovarian cancer	Ovarian cancer	BEFREE	29700285		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	31819475		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	35349479	Stimulate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	35852388	Associate	★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	GWASCAT_DG	25108383		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
leukemia	Leukemia	BEFREE	1348930, 17785556		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	17785556	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	31426381	Stimulate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	LHGDN	12031912, 18410541		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	19563517, 25585874		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	29667179, 34008478	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	30203578		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	29700285		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	19281776		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	19281776, 31819475		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	28464221		★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	17785556		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	32541515	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	19723874, 29700285		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	30196354		★☆☆☆☆ Found in Text Mining only
Ovarian Carcinoma	Ovarian Carcinoma	BEFREE	19281776		★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	19281776, 19723874		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	19723874	Associate	★☆☆☆☆ Found in Text Mining only
Periodontal Diseases	Periodontal disease	Pubtator	37464577	Associate	★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	Pubtator	37464577	Associate	★☆☆☆☆ Found in Text Mining only
Russell-Silver syndrome	Russell-Silver Syndrome	BEFREE	29146936		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	28121923	Associate	★☆☆☆☆ Found in Text Mining only
Werner Syndrome	Werner Syndrome	BEFREE	15561107		★☆☆☆☆ Found in Text Mining only
Werner Syndrome	Werner syndrome	Pubtator	31259468	Associate	★☆☆☆☆ Found in Text Mining only