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P49639 (HXA1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 147. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Homeobox protein Hox-A1
Alternative name(s):
Homeobox protein Hox-1F
Gene names
Name:HOXA1
Synonyms:HOX1F
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length335 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Acts on the anterior body structures. Seems to act in the maintenance and/or generation of hindbrain segments.

Subcellular location

Nucleus.

Involvement in disease

Athabaskan brainstem dysgenesis syndrome (ABDS) [MIM:601536]: Characterized by horizontal gaze palsy, sensorineural deafness, central hypoventilation, and developmental delay. Some patients had swallowing dysfunction, vocal cord paralysis, facial paresis, seizures, and cardiac outflow tract anomalies.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9

Bosley-Salih-Alorainy syndrome (BSAS) [MIM:601536]: A disease characterized by horizontal gaze abnormalities, deafness, facial weakness, vascular malformations of the internal carotid arteries and cardiac outflow trac. Some patients manifest mental retardation and autism spectrum disorder. Affected individuals do not suffer from central hypoventilation.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9

Sequence similarities

Belongs to the Antp homeobox family. Labial subfamily.

Contains 1 homeobox DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainHomeobox
   LigandDNA-binding
   Molecular functionDevelopmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processabducens nerve formation

Inferred from mutant phenotype Ref.9. Source: DFLAT

anterior/posterior pattern specification

Inferred from electronic annotation. Source: Ensembl

artery morphogenesis

Inferred from mutant phenotype Ref.9. Source: DFLAT

central nervous system neuron differentiation

Inferred from electronic annotation. Source: Ensembl

cochlea morphogenesis

Inferred from mutant phenotype Ref.9. Source: DFLAT

cognition

Inferred from direct assay Ref.9. Source: DFLAT

embryonic neurocranium morphogenesis

Inferred from mutant phenotype Ref.9. Source: DFLAT

facial nerve structural organization

Inferred from electronic annotation. Source: Ensembl

facial nucleus development

Inferred from electronic annotation. Source: Ensembl

motor neuron axon guidance

Inferred from electronic annotation. Source: Ensembl

neuromuscular process

Inferred from direct assay Ref.9. Source: DFLAT

optokinetic behavior

Inferred from direct assay Ref.9. Source: DFLAT

outer ear morphogenesis

Inferred from direct assay Ref.9. Source: DFLAT

positive regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

regulation of behavior

Inferred from direct assay Ref.9. Source: DFLAT

rhombomere 3 development

Inferred from electronic annotation. Source: Ensembl

rhombomere 4 development

Inferred from electronic annotation. Source: Ensembl

rhombomere 5 development

Inferred from electronic annotation. Source: Ensembl

semicircular canal formation

Inferred from mutant phenotype Ref.9. Source: DFLAT

sensory perception of sound

Inferred from direct assay Ref.9. Source: DFLAT

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionsequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Hoxa1P090224EBI-740785,EBI-3957603From a different organism.
PRNPP041564EBI-740785,EBI-977302
SUV39H1O434632EBI-740785,EBI-349968

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 3 (identifier: P49639-1)

Also known as: 36 kDa;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 1 (identifier: P49639-2)

Also known as: 14 kDa;

The sequence of this isoform differs from the canonical sequence as follows:
     119-137: VSGGYPQCAPAVYSGNLSS → PPRSLSLPRIGDIFSSADF
     138-335: Missing.
Note: Lacks the homeobox domain.
Isoform 2 (identifier: P49639-3)

Also known as: 24 kDa;

The sequence of this isoform differs from the canonical sequence as follows:
     219-227: KVGEYGYLG → QSCWLVDAP
     228-335: Missing.
Note: Lacks the homeobox domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 335335Homeobox protein Hox-A1
PRO_0000200030

Regions

DNA binding229 – 28860Homeobox
Motif204 – 2096Antp-type hexapeptide
Compositional bias65 – 7410Poly-His
Compositional bias142 – 1465Poly-His
Compositional bias314 – 3174Poly-Ser

Natural variations

Alternative sequence119 – 13719VSGGY…GNLSS → PPRSLSLPRIGDIFSSADF in isoform 1.
VSP_002376
Alternative sequence138 – 335198Missing in isoform 1.
VSP_002377
Alternative sequence219 – 2279KVGEYGYLG → QSCWLVDAP in isoform 2.
VSP_002378
Alternative sequence228 – 335108Missing in isoform 2.
VSP_002379
Natural variant731H → R Frequent polymorphism in individuals of European or African origin. Ref.2 Ref.8
Corresponds to variant rs10951154 [ dbSNP | Ensembl ].
VAR_010305
Natural variant1891E → A.
Corresponds to variant rs17500494 [ dbSNP | Ensembl ].
VAR_030576

Sequences

Sequence LengthMass (Da)Tools
Isoform 3 (36 kDa) [UniParc].

Last modified July 15, 1999. Version 2.
Checksum: 3C3A2D0A59A4181C

FASTA33536,641
        10         20         30         40         50         60 
MDNARMNSFL EYPILSSGDS GTCSARAYPS DHRITTFQSC AVSANSCGGD DRFLVGRGVQ 

        70         80         90        100        110        120 
IGSPHHHHHH HHHHPQPATY QTSGNLGVSY SHSSCGPSYG SQNFSAPYSP YALNQEADVS 

       130        140        150        160        170        180 
GGYPQCAPAV YSGNLSSPMV QHHHHHQGYA GGAVGSPQYI HHSYGQEHQS LALATYNNSL 

       190        200        210        220        230        240 
SPLHASHQEA CRSPASETSS PAQTFDWMKV KRNPPKTGKV GEYGYLGQPN AVRTNFTTKQ 

       250        260        270        280        290        300 
LTELEKEFHF NKYLTRARRV EIAASLQLNE TQVKIWFQNR RMKQKKREKE GLLPISPATP 

       310        320        330 
PGNDEKAEES SEKSSSSPCV PSPGSSTSDT LTTSH 

« Hide

Isoform 1 (14 kDa) [UniParc].

Checksum: 9F0067A9E6AD51DE
Show »

FASTA13714,816
Isoform 2 (24 kDa) [UniParc].

Checksum: 81A54EF51FB0F033
Show »

FASTA22724,489

References

« Hide 'large scale' references
[1]"Structure and function of the HOX A1 human homeobox gene cDNA."
Hong Y.S., Kim S.Y., Bhattacharya A., Pratt D.R., Hong W.K., Tainsky M.A.
Gene 159:209-214(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
Tissue: Ovary.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3), VARIANT ARG-73.
[3]"Human chromosome 7: DNA sequence and biology."
Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S. expand/collapse author list , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
Science 300:767-772(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Tissue: Skin.
[7]"Retinoic acid induces three newly cloned HOXA1 transcripts in MCF7 breast cancer cells."
Chariot A., Moreau L., Senterre G., Sobel M., Castronovo V.
Biochem. Biophys. Res. Commun. 215:713-720(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 6-335 (ISOFORMS 1; 2 AND 3).
[8]"Discovery of allelic variants of HOXA1 and HOXB1: genetic susceptibility to autism spectrum disorders."
Ingram J.L., Stodgell C.J., Hyman S.L., Figlewicz D.A., Weitkamp L.R., Rodier P.M.
Teratology 62:393-405(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT ARG-73.
[9]"Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development."
Tischfield M.A., Bosley T.M., Salih M.A.M., Alorainy I.A., Sener E.C., Nester M.J., Oystreck D.T., Chan W.-M., Andrews C., Erickson R.P., Engle E.C.
Nat. Genet. 37:1035-1037(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN ABDS AND BSAS.
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U10421 mRNA. Translation: AAA86954.1.
AK313514 mRNA. Translation: BAG36294.1.
AC004079 Genomic DNA. Translation: AAS00374.1.
CH236948 Genomic DNA. Translation: EAL24228.1.
CH471073 Genomic DNA. Translation: EAW93861.1.
BC032547 mRNA. Translation: AAH32547.1.
U37431 mRNA. Translation: AAC50248.1.
U37431 mRNA. Translation: AAC50249.1.
U37431 mRNA. Translation: AAC50250.1.
S79869 mRNA. Translation: AAB35424.2.
S79871 mRNA. Translation: AAB35425.1.
S79910 mRNA. Translation: AAB35423.2.
PIRG01448.
RefSeqNP_005513.1. NM_005522.4.
NP_705873.2. NM_153620.2.
UniGeneHs.67397.

3D structure databases

ProteinModelPortalP49639.
SMRP49639. Positions 202-290.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109438. 54 interactions.
IntActP49639. 16 interactions.
MINTMINT-1437157.
STRING9606.ENSP00000343246.

Chemistry

BindingDBP49639.

PTM databases

PhosphoSiteP49639.

Polymorphism databases

DMDM6166216.

Proteomic databases

PaxDbP49639.
PRIDEP49639.

Protocols and materials databases

DNASU3198.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000343060; ENSP00000343246; ENSG00000105991.
GeneID3198.
KEGGhsa:3198.
UCSCuc003syd.3. human. [P49639-2]
uc003sye.3. human. [P49639-1]
uc022aao.1. human. [P49639-3]

Organism-specific databases

CTD3198.
GeneCardsGC07M027099.
HGNCHGNC:5099. HOXA1.
HPAHPA004933.
MIM142955. gene.
601536. phenotype.
neXtProtNX_P49639.
Orphanet69739. Athabaskan brainstem dysgenesis syndrome.
69737. Bosley-Salih-Alorainy syndrome.
PharmGKBPA29376.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG236971.
HOGENOMHOG000247020.
HOVERGENHBG006089.
InParanoidP49639.
KOK09301.
OrthoDBEOG7PK91P.
TreeFamTF317730.

Gene expression databases

ArrayExpressP49639.
BgeeP49639.
CleanExHS_HOXA1.
GenevestigatorP49639.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
InterProIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSPR00024. HOMEOBOX.
SMARTSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiHomeobox_A1.
GenomeRNAi3198.
NextBio12718.
PROP49639.
SOURCESearch...

Entry information

Entry nameHXA1_HUMAN
AccessionPrimary (citable) accession number: P49639
Secondary accession number(s): A4D184, B2R8U7, O43363
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: July 15, 1999
Last modified: March 19, 2014
This is version 147 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM

Vertebrate homeotic Hox proteins

Nomenclature of vertebrate homeotic Hox proteins and list of entries