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Protein

Homeobox protein Hox-A1a

Gene

hoxa1a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi225 – 28460HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. sequence-specific DNA binding Source: InterPro

GO - Biological processi

  1. multicellular organismal development Source: UniProtKB-KW
  2. regulation of transcription, DNA-templated Source: UniProtKB-KW
  3. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Homeobox protein Hox-A1a
Short name:
Hox-A1
Gene namesi
Name:hoxa1a
Synonyms:hoxa1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Chromosome 19

Organism-specific databases

ZFINiZDB-GENE-000823-5. hoxa1a.

Subcellular locationi

Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 329329Homeobox protein Hox-A1aPRO_0000200033Add
BLAST

Expressioni

Gene expression databases

BgeeiQ98SI1.

Structurei

3D structure databases

ProteinModelPortaliQ98SI1.
SMRiQ98SI1. Positions 198-286.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi200 – 2056Antp-type hexapeptide

Sequence similaritiesi

Belongs to the Antp homeobox family. Labial subfamily.Curated
Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiNOG236971.
GeneTreeiENSGT00760000118940.
HOGENOMiHOG000247020.
HOVERGENiHBG006089.
InParanoidiQ98SI1.
KOiK09301.
OMAiCAVSANS.
OrthoDBiEOG7PK91P.
PhylomeDBiQ98SI1.
TreeFamiTF317730.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q98SI1-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MSTFLDFSSI SGGGDGGSGG SCSVRAFHGD HGLSTFQSSC AVRLNSCSGD
60 70 80 90 100
ERFMSNISSQ DVINSQPQQA GSYQSPGTLS ITYSAHPSYG TQSFCTGYNH
110 120 130 140 150
YALNQDVESS VSFPQCGPLV YSGNISSTVV QHRHHRHGYS SGNVHLHGQF
160 170 180 190 200
QYGSATYGNS SDQANLTFVA GCSNPLSPLH VPHHDACCSP LSDGVPTGQT
210 220 230 240 250
FDWMKVKRNP PKTGKAGEYG FGGQPNTVRT NFSTKQLTEL EKEFHFNKYL
260 270 280 290 300
TRARRVEIAA SLQLNETQVK IWFQNRRMKQ KKREKEGLLP KSLSEQKDGL
310 320
EKTEDASEKS PSAPSTPSPS PTVEAYSSN
Length:329
Mass (Da):35,737
Last modified:June 1, 2001 - v1
Checksum:iCBF2C722F50A85D5
GO
Isoform 2 (identifier: Q98SI1-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     158-192: Missing.

Show »
Length:294
Mass (Da):32,178
Checksum:i8A603E507F410727
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1 – 2828MSTFL…VRAFH → MEVAGARAQSGRSQ(PubMed:9831563)CuratedAdd
BLAST
Sequence conflicti296 – 2961Q → E in CAC34566. (PubMed:11493564)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei158 – 19235Missing in isoform 2. 1 PublicationVSP_012678Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ306430 mRNA. Translation: CAC34565.1.
AJ306431 mRNA. Translation: CAC34566.1.
AF071243 Genomic DNA. Translation: AAD15937.1.
AL645756 Genomic DNA. Translation: CAD52136.1.
AL645756 Genomic DNA. Translation: CAD52137.1.
CR382300 Genomic DNA. Translation: CAK10852.1.
DQ060531 mRNA. Translation: AAY67909.1.
RefSeqiNP_571611.1. NM_131536.2. [Q98SI1-1]
XP_005159579.1. XM_005159522.2. [Q98SI1-2]
XP_009292446.1. XM_009294171.1. [Q98SI1-1]
XP_009292447.1. XM_009294172.1. [Q98SI1-1]
UniGeneiDr.83046.

Genome annotation databases

EnsembliENSDART00000080456; ENSDARP00000074905; ENSDARG00000057721. [Q98SI1-2]
ENSDART00000080461; ENSDARP00000074910; ENSDARG00000057721. [Q98SI1-1]
GeneIDi58051.
KEGGidre:58051.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ306430 mRNA. Translation: CAC34565.1.
AJ306431 mRNA. Translation: CAC34566.1.
AF071243 Genomic DNA. Translation: AAD15937.1.
AL645756 Genomic DNA. Translation: CAD52136.1.
AL645756 Genomic DNA. Translation: CAD52137.1.
CR382300 Genomic DNA. Translation: CAK10852.1.
DQ060531 mRNA. Translation: AAY67909.1.
RefSeqiNP_571611.1. NM_131536.2. [Q98SI1-1]
XP_005159579.1. XM_005159522.2. [Q98SI1-2]
XP_009292446.1. XM_009294171.1. [Q98SI1-1]
XP_009292447.1. XM_009294172.1. [Q98SI1-1]
UniGeneiDr.83046.

3D structure databases

ProteinModelPortaliQ98SI1.
SMRiQ98SI1. Positions 198-286.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000080456; ENSDARP00000074905; ENSDARG00000057721. [Q98SI1-2]
ENSDART00000080461; ENSDARP00000074910; ENSDARG00000057721. [Q98SI1-1]
GeneIDi58051.
KEGGidre:58051.

Organism-specific databases

CTDi58051.
ZFINiZDB-GENE-000823-5. hoxa1a.

Phylogenomic databases

eggNOGiNOG236971.
GeneTreeiENSGT00760000118940.
HOGENOMiHOG000247020.
HOVERGENiHBG006089.
InParanoidiQ98SI1.
KOiK09301.
OMAiCAVSANS.
OrthoDBiEOG7PK91P.
PhylomeDBiQ98SI1.
TreeFamiTF317730.

Miscellaneous databases

NextBioi20892315.
PROiQ98SI1.

Gene expression databases

BgeeiQ98SI1.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes."
    McClintock J.M., Carlson R., Mann D.M., Prince V.E.
    Development 128:2471-2484(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  4. "Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a."
    Corredor-Adamez M., Welten M.C.M., Spaink H.P., Jeffery J.E., Schoon R.T., de Bakker M.A.G., Bagowski C.P., Meijer A.H., Verbeek F.J., Richardson M.K.
    Evol. Dev. 7:362-375(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 136-224.
    Strain: Tuebingen.

Entry informationi

Entry nameiHXA1A_DANRE
AccessioniPrimary (citable) accession number: Q98SI1
Secondary accession number(s): Q1L968
, Q4PRB2, Q8AWZ1, Q98SI0, Q9YGT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2005
Last sequence update: June 1, 2001
Last modified: January 7, 2015
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Vertebrate homeotic Hox proteins
    Nomenclature of vertebrate homeotic Hox proteins and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.