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Protein

Homeobox protein Hox-D4a

Gene

hoxd4a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 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.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi146 – 20560HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • angiogenesis Source: ZFIN
  • definitive hemopoiesis Source: ZFIN
  • primitive hemopoiesis Source: ZFIN
  • transcription, DNA-templated Source: UniProtKB-KW
  • vasculogenesis Source: ZFIN
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-D4a
Short name:
Hox-D4
Gene namesi
Name:hoxd4a
Synonyms:hoxd4
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-980526-214. hoxd4a.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 236236Homeobox protein Hox-D4aPRO_0000200214Add
BLAST

Proteomic databases

PaxDbiO57374.

Expressioni

Developmental stagei

At the 10-somite stage, barely expressed in the paraxial mesoderm. At the 20-somite stage, expressed in the developing CNS with an anterior expression limit at the rhombomere 6/7 boundary.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000076791.

Structurei

3D structure databases

ProteinModelPortaliO57374.
SMRiO57374. Positions 120-206.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi125 – 1306Antp-type hexapeptide

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiKOG0489. Eukaryota.
ENOG410ZTBY. LUCA.
HOVERGENiHBG016849.
InParanoidiO57374.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017995. Homeobox_antennapedia.
IPR001827. Homeobox_Antennapedia_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00025. ANTENNAPEDIA.
PR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00032. ANTENNAPEDIA. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O57374-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMSSYMVNS KYVDPKFPPC EEYSQNSYIP EQSPGYYSPS QDTDFQHPGI
60 70 80 90 100
YSRSNYSEQP YICSTVQGSS VQPRGHVQDQ ASTPSPFPAQ TEQCPAVQIS
110 120 130 140 150
GSRTCGQQQN TKTQNGIPTK QPAVVYPWMK KVHVTTVNPD YTGPEPKRSR
160 170 180 190 200
TAYTRQQVLE LEKEFHFNRY LTRRRRIESA HTLSLSERQI KIWFQNRRMK
210 220 230
WKKDHKLPNT KGRSASVGNQ HAQHAQKDSQ TEITTL
Length:236
Mass (Da):27,132
Last modified:July 15, 1999 - v2
Checksum:iAAEB8C7F34F17B5E
GO

Sequence cautioni

The sequence CAA74883.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti105 – 1051C → G in AAY67943 (PubMed:16174031).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14548 mRNA. Translation: CAA74883.1. Different initiation.
AY168642 Genomic DNA. Translation: AAN86981.1.
DQ060565 mRNA. Translation: AAY67943.1.
UniGeneiDr.75800.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14548 mRNA. Translation: CAA74883.1. Different initiation.
AY168642 Genomic DNA. Translation: AAN86981.1.
DQ060565 mRNA. Translation: AAY67943.1.
UniGeneiDr.75800.

3D structure databases

ProteinModelPortaliO57374.
SMRiO57374. Positions 120-206.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000076791.

Proteomic databases

PaxDbiO57374.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

ZFINiZDB-GENE-980526-214. hoxd4a.

Phylogenomic databases

eggNOGiKOG0489. Eukaryota.
ENOG410ZTBY. LUCA.
HOVERGENiHBG016849.
InParanoidiO57374.

Miscellaneous databases

PROiO57374.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017995. Homeobox_antennapedia.
IPR001827. Homeobox_Antennapedia_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00025. ANTENNAPEDIA.
PR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00032. ANTENNAPEDIA. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk."
    Prince V.E., Joly L., Ekker M., Ho R.K.
    Development 125:407-420(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
    Tissue: Embryo.
  2. "The role of a retinoic acid response element in establishing the anterior neural expression border of Hoxd4 transgenes."
    Nolte C., Amores A., Nagy Kovacs E., Postlethwait J., Featherstone M.
    Mech. Dev. 120:325-335(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "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 63-144.
    Strain: Tuebingen.

Entry informationi

Entry nameiHXD4A_DANRE
AccessioniPrimary (citable) accession number: O57374
Secondary accession number(s): Q4PR78
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: July 15, 1999
Last modified: February 17, 2016
This is version 110 of the entry and version 2 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

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 one 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.