HOXA1 (homeobox A1)

Gene

• Entrez ID: 3198
• Gene name: Homeobox A1
• Gene symbol: HOXA1
• Synonyms (NCBI Gene): BSAS, HOX1, HOX1F
• Disease Acronyms (UniProt): BSAS
• 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
MIRT001140	hsa-miR-10a-5p	Luciferase reporter assay, qRT-PCR, Western blot	16549775
MIRT000152	hsa-miR-210-3p	Luciferase reporter assay	19782034
MIRT001140	hsa-miR-10a-5p	Review	20029422
MIRT004641	hsa-miR-10b-5p	Review	20029422
MIRT001140	hsa-miR-10a-5p	Reporter assay;Other	16549775
MIRT001140	hsa-miR-10a-5p	qRT-PCR, Western blot	24498243
MIRT054544	hsa-miR-100-5p	Flow, Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	24559685
MIRT054544	hsa-miR-100-5p	Flow, Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	24559685
MIRT054544	hsa-miR-100-5p	ChIP-seq, Immunohistochemistry, In situ hybridization, Luciferase reporter assay, Microarray, qRT-PCR, Western blot	24586203
MIRT054544	hsa-miR-100-5p	ChIP-seq, Immunohistochemistry, In situ hybridization, Luciferase reporter assay, Microarray, qRT-PCR, Western blot	24586203
MIRT054708	hsa-miR-99a-5p	Luciferase reporter assay, Microarray, qRT-PCR, Western blot	24312487
MIRT529277	hsa-miR-8080	PAR-CLIP	22012620
MIRT529276	hsa-miR-6830-5p	PAR-CLIP	22012620
MIRT529275	hsa-miR-561-5p	PAR-CLIP	22012620
MIRT529274	hsa-miR-498	PAR-CLIP	22012620
MIRT443420	hsa-miR-455-5p	PAR-CLIP	22100165
MIRT443419	hsa-miR-8060	PAR-CLIP	22100165
MIRT443418	hsa-miR-6887-3p	PAR-CLIP	22100165
MIRT443417	hsa-miR-6795-3p	PAR-CLIP	22100165
MIRT443416	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT443415	hsa-miR-5189-3p	PAR-CLIP	22100165
MIRT443413	hsa-miR-1227-3p	PAR-CLIP	22100165
MIRT443414	hsa-miR-7154-5p	PAR-CLIP	22100165
MIRT443412	hsa-miR-6826-3p	PAR-CLIP	22100165
MIRT054708	hsa-miR-99a-5p	Luciferase reporter assay, qRT-PCR, Western blot	28228659
MIRT054708	hsa-miR-99a-5p	Luciferase reporter assay, qRT-PCR, Western blot	28228659
MIRT054708	hsa-miR-99a-5p	Luciferase reporter assay, qRT-PCR, Western blot	28228659
MIRT054708	hsa-miR-99a-5p	Luciferase reporter assay, qRT-PCR, Western blot	26417931
MIRT054708	hsa-miR-99a-5p	Luciferase reporter assay, qRT-PCR, Western blot	26417931
MIRT054544	hsa-miR-100-5p	Luciferase reporter assay, Western blotting, qRT-PCR	32364673
MIRT737404	hsa-miR-100-3p	Luciferase reporter assay, Western blotting, RNA-seq, qRT-PCR	32021301
MIRT529277	hsa-miR-8080	PAR-CLIP	22012620
MIRT529276	hsa-miR-6830-5p	PAR-CLIP	22012620
MIRT529275	hsa-miR-561-5p	PAR-CLIP	22012620
MIRT529274	hsa-miR-498	PAR-CLIP	22012620
MIRT443420	hsa-miR-455-5p	PAR-CLIP	22100165
MIRT443419	hsa-miR-8060	PAR-CLIP	22100165
MIRT443418	hsa-miR-6887-3p	PAR-CLIP	22100165
MIRT443417	hsa-miR-6795-3p	PAR-CLIP	22100165
MIRT443416	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT443415	hsa-miR-5189-3p	PAR-CLIP	22100165
MIRT443413	hsa-miR-1227-3p	PAR-CLIP	22100165
MIRT443414	hsa-miR-7154-5p	PAR-CLIP	22100165
MIRT443412	hsa-miR-6826-3p	PAR-CLIP	22100165
MIRT1053119	hsa-miR-100	CLIP-seq
MIRT1053120	hsa-miR-3119	CLIP-seq
MIRT1053121	hsa-miR-3140-3p	CLIP-seq
MIRT1053122	hsa-miR-3179	CLIP-seq
MIRT1053123	hsa-miR-3667-5p	CLIP-seq
MIRT1053124	hsa-miR-4652-3p	CLIP-seq
MIRT1053125	hsa-miR-556-3p	CLIP-seq
MIRT1053126	hsa-miR-99a	CLIP-seq
MIRT1053127	hsa-miR-99b	CLIP-seq
MIRT2012090	hsa-miR-4686	CLIP-seq
MIRT2012091	hsa-miR-513a-3p	CLIP-seq
MIRT2244351	hsa-miR-1257	CLIP-seq
MIRT2244352	hsa-miR-4279	CLIP-seq
MIRT2244353	hsa-miR-4452	CLIP-seq
MIRT2244354	hsa-miR-4459	CLIP-seq
MIRT2244355	hsa-miR-4677-3p	CLIP-seq
MIRT2244356	hsa-miR-4679	CLIP-seq
MIRT2244357	hsa-miR-4722-5p	CLIP-seq
MIRT2244358	hsa-miR-4779	CLIP-seq
MIRT2547257	hsa-miR-1225-5p	CLIP-seq
MIRT2547258	hsa-miR-1252	CLIP-seq
MIRT2547259	hsa-miR-1253	CLIP-seq
MIRT2547260	hsa-miR-1273d	CLIP-seq
MIRT2547261	hsa-miR-1538	CLIP-seq
MIRT2547262	hsa-miR-200b	CLIP-seq
MIRT2547263	hsa-miR-200c	CLIP-seq
MIRT2547264	hsa-miR-218	CLIP-seq
MIRT2547265	hsa-miR-2355-5p	CLIP-seq
MIRT2547266	hsa-miR-28-5p	CLIP-seq
MIRT2547267	hsa-miR-3132	CLIP-seq
MIRT2547268	hsa-miR-3139	CLIP-seq
MIRT2547269	hsa-miR-3159	CLIP-seq
MIRT2547270	hsa-miR-3190	CLIP-seq
MIRT2547271	hsa-miR-3202	CLIP-seq
MIRT2547272	hsa-miR-3607-3p	CLIP-seq
MIRT2547273	hsa-miR-3688-3p	CLIP-seq
MIRT2547274	hsa-miR-369-3p	CLIP-seq
MIRT2547275	hsa-miR-3936	CLIP-seq
MIRT2547276	hsa-miR-3978	CLIP-seq
MIRT2547277	hsa-miR-4267	CLIP-seq
MIRT2547278	hsa-miR-429	CLIP-seq
MIRT2547279	hsa-miR-4311	CLIP-seq
MIRT2547280	hsa-miR-4318	CLIP-seq
MIRT2547281	hsa-miR-4427	CLIP-seq
MIRT2547282	hsa-miR-4435	CLIP-seq
MIRT2547283	hsa-miR-4451	CLIP-seq
MIRT2547284	hsa-miR-4533	CLIP-seq
MIRT2547285	hsa-miR-4662a-3p	CLIP-seq
MIRT2547286	hsa-miR-4680-3p	CLIP-seq
MIRT2547287	hsa-miR-4694-3p	CLIP-seq
MIRT2547288	hsa-miR-4719	CLIP-seq
MIRT2547289	hsa-miR-4740-3p	CLIP-seq
MIRT2547290	hsa-miR-4745-3p	CLIP-seq
MIRT2547291	hsa-miR-522	CLIP-seq
MIRT2547292	hsa-miR-555	CLIP-seq
MIRT2547293	hsa-miR-590-3p	CLIP-seq
MIRT2547294	hsa-miR-636	CLIP-seq
MIRT2547295	hsa-miR-656	CLIP-seq
MIRT2547296	hsa-miR-663b	CLIP-seq
MIRT2547297	hsa-miR-665	CLIP-seq
MIRT2547298	hsa-miR-708	CLIP-seq
MIRT2682422	hsa-miR-1227	CLIP-seq
MIRT2547258	hsa-miR-1252	CLIP-seq
MIRT2682423	hsa-miR-1255a	CLIP-seq
MIRT2682424	hsa-miR-1255b	CLIP-seq
MIRT2682425	hsa-miR-181a	CLIP-seq
MIRT2682426	hsa-miR-181b	CLIP-seq
MIRT2682427	hsa-miR-181c	CLIP-seq
MIRT2682428	hsa-miR-181d	CLIP-seq
MIRT2682429	hsa-miR-198	CLIP-seq
MIRT2682430	hsa-miR-23a	CLIP-seq
MIRT2682431	hsa-miR-23b	CLIP-seq
MIRT2682432	hsa-miR-23c	CLIP-seq
MIRT2682433	hsa-miR-3160-3p	CLIP-seq
MIRT2547270	hsa-miR-3190	CLIP-seq
MIRT2547271	hsa-miR-3202	CLIP-seq
MIRT2682434	hsa-miR-323-3p	CLIP-seq
MIRT2682435	hsa-miR-326	CLIP-seq
MIRT2682436	hsa-miR-330-5p	CLIP-seq
MIRT2682437	hsa-miR-3647-3p	CLIP-seq
MIRT2682438	hsa-miR-3663-5p	CLIP-seq
MIRT2682439	hsa-miR-3691-3p	CLIP-seq
MIRT2682440	hsa-miR-4262	CLIP-seq
MIRT2547277	hsa-miR-4267	CLIP-seq
MIRT2682441	hsa-miR-4289	CLIP-seq
MIRT2547280	hsa-miR-4318	CLIP-seq
MIRT2682442	hsa-miR-4487	CLIP-seq
MIRT2682443	hsa-miR-4528	CLIP-seq
MIRT2547284	hsa-miR-4533	CLIP-seq
MIRT2547285	hsa-miR-4662a-3p	CLIP-seq
MIRT2682444	hsa-miR-4694-5p	CLIP-seq
MIRT2682445	hsa-miR-4782-5p	CLIP-seq
MIRT2682446	hsa-miR-493	CLIP-seq
MIRT2682447	hsa-miR-558	CLIP-seq
MIRT2682448	hsa-miR-593	CLIP-seq
MIRT2682449	hsa-miR-664	CLIP-seq

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	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
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	15665309
GO:0005515	Function	Protein binding	IPI	16189514, 18482256, 23088713, 23455924, 25416956, 25910212, 29892012, 30886144, 31515488, 32296183, 32814053
GO:0005634	Component	Nucleus	IBA	21873635
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007275	Process	Multicellular organism development	TAS	7622051
GO:0007605	Process	Sensory perception of sound	IDA	16155570
GO:0007634	Process	Optokinetic behavior	IDA	16155570
GO:0009653	Process	Anatomical structure morphogenesis	IMP	16155570
GO:0021599	Process	Abducens nerve formation	IMP	16155570
GO:0042473	Process	Outer ear morphogenesis	IDA	16155570
GO:0042802	Function	Identical protein binding	IPI	21516116, 25416956, 30886144, 32296183
GO:0043565	Function	Sequence-specific DNA binding	IDA	23332764
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	15665309
GO:0048702	Process	Embryonic neurocranium morphogenesis	IMP	16155570
GO:0048839	Process	Inner ear development	IMP	16155570
GO:0048844	Process	Artery morphogenesis	IMP	16155570
GO:0050795	Process	Regulation of behavior	IDA	16155570
GO:0050890	Process	Cognition	IDA	16155570
GO:0050905	Process	Neuromuscular process	IDA	16155570
GO:0060840	Process	Artery development	IMP	16155570
GO:0060876	Process	Semicircular canal formation	IMP	16155570
GO:0090102	Process	Cochlea development	IMP	16155570
GO:0090103	Process	Cochlea morphogenesis	IMP	16155570
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 142955
• HGNC: 5099
• e!Ensembl: ENSG00000105991

Protein

• UniProt ID: P49639
• Protein name: Homeobox protein Hox-A1 (Homeobox protein Hox-1F)
• Protein function: Sequence-specific transcription factor (By similarity). Regulates multiple developmental processes including brainstem, inner and outer ear, abducens nerve and cardiovascular development and morphogenesis as well as cognition and behavior (PubMe
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00046	Homeodomain	230 → 286	Homeodomain	Domain

• Sequence:

  MDNARMNSFLEYPILSSGDSGTCSARAYPSDHRITTFQSCAVSANSCGGDDRFLVGRGVQ
  IGSPHHHHHHHHHHPQPATYQTSGNLGVSYSHSSCGPSYGSQNFSAPYSPYALNQEADVS
  GGYPQCAPAVYSGNLSSPMVQHHHHHQGYAGGAVGSPQYIHHSYGQEHQSLALATYNNSL
  SPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGKVGEYGYLGQPNAVRTNFTTKQ
  LTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLLPISPATP
  PGNDEKAEESSEKSSSSPCVPSPGSSTSDTLTTSH

• Sequence length: 335

Pathways

KEGG:

Signaling pathways regulating pluripotency of stem cells

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Anencephaly	Cranioschisis	rs773607884	10529420
Autism	Autistic Disorder	rs121964908, rs62643608, rs181327458, rs797046134, rs869312704, rs1555013332, rs876657679, rs1057518999, rs1057518658, rs771827120, rs1555187899, rs773080572, rs753871454, rs1684130791, rs1684180699, rs1553510219, rs1684182454, rs1559060428, rs1553510677, rs1576352885, rs1574152522, rs1574152672, rs1696658542	11091361
Bosley-salih-alorainy syndrome	Bosley-Salih-Alorainy Syndrome, Bosley-Salih-Alorainy syndrome	rs769152039, rs104894017, rs1562700083	24239177, 17875913
Congenital heart defects	Congenital Heart Defects	rs267607101, rs121434422, rs387906498, rs397509416, rs587777371, rs587777372, rs587777374, rs367537998, rs797044882, rs886041730, rs768027510, rs1064793873, rs1555447012, rs1554263268, rs1554263321, rs1555223294, rs782051102, rs1555896779, rs1555896778, rs1555897088, rs374016704, rs1555446983, rs1479104927, rs1562443558, rs755445139, rs1581616817, rs1581655293, rs1899172049	21940751
Developmental delay	Gross motor development delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Hearing loss	Sensorineural Hearing Loss (disorder)	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359, rs180177151, rs180177154, rs180177153, rs35689081, rs35887622, rs80338944, rs104894396, rs104894398, rs80338947, rs80338948, rs80338942, rs104894402, rs104894403, rs80338945, rs28931594, rs80338940, rs80338941, rs80356590, rs80338950, rs387906706, rs387906707, rs387906708, rs398122848, rs387907016, rs587776894, rs387907088, rs397515411, rs370965183, rs398122930, rs199897298, rs111033187, rs111033448, rs199606180, rs111033284, rs397516413, rs111033305, rs111033220, rs111033256, rs111033297, rs111033253, rs104894408, rs111033295, rs397516874, rs76434661, rs111033335, rs397517323, rs111033247, rs367928692, rs374793617, rs143939430, rs397515605, rs80338939, rs200656442, rs779748859, rs587781261, rs587781262, rs143343083, rs200147906, rs730880338, rs797044491, rs146281367, rs756484720, rs869025593, rs201306709, rs540895576, rs777777359, rs879255246, rs1554358720, rs142498437, rs377145777, rs1057517519, rs779077039, rs952741388, rs1060499797, rs764139009, rs1060499590, rs1064794012, rs1064797115, rs756790858, rs775633137, rs1554952443, rs1554952193, rs782063761, rs1199012623, rs756147087, rs1555648043, rs1555661490, rs1553196233, rs781546107, rs111033190, rs775428246, rs782539587, rs537227442, rs148695069, rs1554835827, rs953422571, rs1554834186, rs1554834161, rs1554835103, rs1554577339, rs1554577402, rs768471577, rs782279338, rs781951909, rs998045226, rs375759781, rs755804651, rs1557458426, rs767797828, rs538027448, rs1559366084, rs367688416, rs1558480402, rs1558490542, rs1559870857, rs1560690591, rs1561299289, rs1562817224, rs1562817529, rs1562822565, rs1562835391, rs1564113368, rs1564554255, rs773851192, rs1564555240, rs761261855, rs1564805114, rs1565522273, rs1565127413, rs781790246, rs1565430886, rs1565469959, rs746667217, rs1565819402, rs1565855932, rs150529554, rs1567939793, rs201866631, rs754472294, rs1559372512, rs1558464965, rs1558488902, rs775062249, rs1226171550, rs1561590396, rs765574676, rs762876554, rs757327146, rs1564949059, rs1565519673, rs368050948, rs1565541888, rs781989117, rs1565402473, rs750358148, rs1386887007, rs1209665716, rs1567641234, rs1237955948, rs1569042782, rs752672077, rs146689036, rs1560070780, rs149712664, rs1564556995, rs762226905, rs773573968, rs1568528171, rs1198256157, rs377267777, rs370564476, rs1577876794, rs747787770, rs759432278, rs1043716893, rs1581138934, rs2033773650, rs1421964916, rs771766431, rs780917129, rs1895773215, rs1895769400, rs761543680, rs1565920060
Human hoxa1 syndromes	Athabaskan brainstem dysgenesis	rs769152039, rs104894018	16155570, 24239177, 18412118, 12833395

Unknown
Disease term	Disease name	Evidence	References	Source
Mental retardation	syndromic intellectual disability			GenCC
Bosley-Salih-Alorainy Syndrome	Bosley-Salih-Alorainy syndrome			GenCC
Multiple Sclerosis	Multiple Sclerosis			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma	Associate	17967182
Adenocarcinoma in Situ	Associate	21731750
Adenocarcinoma of Lung	Associate	17967182, 35633885
Anthropophobia	Associate	33048872
Athabaskan brainstem dysgenesis	Associate	17875913, 18412118
Autism Spectrum Disorder	Associate	22359339
Autistic Disorder	Associate	20227628, 22359339
Breast Neoplasms	Associate	16373333, 22037257, 26417931, 27382069, 30259272, 34180753, 7488013, 8670198
Carcinogenesis	Associate	22498108, 28893210
Carcinoma Hepatocellular	Associate	30168613
Carcinoma Non Small Cell Lung	Stimulate	29658571
Cardiovascular Abnormalities	Associate	18412118
Carotid Stenosis	Associate	20075099
Central Nervous System Vascular Malformations	Associate	17197532
Cholangiocarcinoma	Associate	17550320, 29484968
Cognition Disorders	Associate	17197532
Colorectal Neoplasms	Associate	29137689
Congenital central hypoventilation syndrome	Associate	20227628
Conotruncal cardiac defects	Associate	20227628
Deafness	Associate	17197532
Deafness Congenital with Inner Ear Agenesis Microtia and Microdontia	Associate	20075099
Duane Retraction Syndrome	Associate	17197532
gaze palsy familial horizontal with progressive scoliosis	Associate	18412118, 20227628
Giant Cell Tumor of Bone	Associate	29164581
Glioma	Stimulate	35349479
Hearing Loss Sensorineural	Associate	20227628
Heart Defects Congenital	Associate	18412118
Hepatitis C	Stimulate	24789793
HIV Infections	Associate	33048872
Intellectual Disability	Associate	18412118, 20227628
Keratoderma Palmoplantar	Associate	30168613
Labyrinth Diseases	Associate	20075099
Leiomyosarcoma	Associate	28893210
Leukemia Myeloid Acute	Associate	31426381
Leukemia Promyelocytic Acute	Associate	12893766
Leukoplakia	Stimulate	38408418
Lung Neoplasms	Associate	17967182, 22693540
Lung Neoplasms	Stimulate	35633885
Lupus Erythematosus Systemic	Associate	40185033
Lymphoma Non Hodgkin	Associate	35677036
Movement Disorders	Associate	20227628
Muscle Weakness	Associate	20227628
Neoplasms	Associate	16373333, 22498108, 24498243, 26417931, 27382069, 28481029, 29484968, 29658571, 34606634
Ocular Motility Disorders	Associate	20075099
Ovarian Neoplasms	Associate	33332731
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	31204714
Retinoblastoma	Associate	32561925
Small Cell Lung Carcinoma	Associate	26707824
Squamous Cell Carcinoma of Head and Neck	Associate	22498108, 33285674, 34406843
Stomach Neoplasms	Associate	18158559, 24498243
Syndrome	Associate	17875913
Uterine Cervical Neoplasms	Associate	12824890, 27296950, 30896864, 31114990, 34606634