Reviewed, UniProtKB/Swiss-Prot Q98SI1 (HXA1A_DANRE)

Names and origin

Protein names

Recommended name:
    Homeobox protein Hox-A1a
      Short name=Hox-A1

Gene names

Name:	hoxa1a
Synonyms:	hoxa1

Organism

Danio rerio (Zebrafish) (Brachydanio rerio)

Taxonomic identifier

7955 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Cyprinidae › Danio

Protein attributes

Sequence length	329 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at transcript 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 By similarity.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the Antp homeobox family. Labial subfamily. Contains 1 homeobox DNA-binding domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Homeobox
Ligand	DNA-binding
Molecular function	Developmental protein
Gene Ontology (GO)
Biological process	multicellular organismal development Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro transcription factor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q98SI1-1)

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 2 (identifier: Q98SI1-2)

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

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 329	329	Homeobox protein Hox-A1a		PRO_0000200033
Regions
	DNA binding	225 – 284	60	Homeobox
	Motif	200 – 205	6	Antp-type hexapeptide
Natural variations
	Alternative sequence	158 – 192	35	Missing in isoform 2.		VSP_012678
Experimental info
	Sequence conflict	1 – 28	28	MSTFL…VRAFH → MEVAGARAQSGRSQ Ref.2
	Sequence conflict	296	1	Q → E in CAC34566. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 1, 2001. Version 1. Checksum: CBF2C722F50A85D5	FASTA	329	35,737
	10 20 30 40 50 60 MSTFLDFSSI SGGGDGGSGG SCSVRAFHGD HGLSTFQSSC AVRLNSCSGD ERFMSNISSQ 70 80 90 100 110 120 DVINSQPQQA GSYQSPGTLS ITYSAHPSYG TQSFCTGYNH YALNQDVESS VSFPQCGPLV 130 140 150 160 170 180 YSGNISSTVV QHRHHRHGYS SGNVHLHGQF QYGSATYGNS SDQANLTFVA GCSNPLSPLH 190 200 210 220 230 240 VPHHDACCSP LSDGVPTGQT FDWMKVKRNP PKTGKAGEYG FGGQPNTVRT NFSTKQLTEL 250 260 270 280 290 300 EKEFHFNKYL TRARRVEIAA SLQLNETQVK IWFQNRRMKQ KKREKEGLLP KSLSEQKDGL 310 320 EKTEDASEKS PSAPSTPSPS PTVEAYSSN
	Isoform 2. Checksum: 8A603E507F410727	FASTA	294	32,178
	10 20 30 40 50 60 MSTFLDFSSI SGGGDGGSGG SCSVRAFHGD HGLSTFQSSC AVRLNSCSGD ERFMSNISSQ 70 80 90 100 110 120 DVINSQPQQA GSYQSPGTLS ITYSAHPSYG TQSFCTGYNH YALNQDVESS VSFPQCGPLV 130 140 150 160 170 180 YSGNISSTVV QHRHHRHGYS SGNVHLHGQF QYGSATYDGV PTGQTFDWMK VKRNPPKTGK 190 200 210 220 230 240 AGEYGFGGQP NTVRTNFSTK QLTELEKEFH FNKYLTRARR VEIAASLQLN ETQVKIWFQN 250 260 270 280 290 RRMKQKKREK EGLLPKSLSE QKDGLEKTED ASEKSPSAPS TPSPSPTVEA YSSN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 11493564] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
[2]	"Zebrafish hox clusters and vertebrate genome evolution." Amores A., Force A., Yan Y.-L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V.E., Wang Y.-L., Westerfield M., Ekker M., Postlethwait J.H. Science 282:1711-1714(1998) [PubMed: 9831563] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	The Danio rerio sequencing project at the Sanger Institute Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AB and 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: 16174031] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 136-224. Strain: Tuebingen.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	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.
IPI	IPI00494329. IPI00494805.
RefSeq	NP_571611.1.
UniGene	Dr.83046
3D structure databases
ModBase	Search...
Genome annotation databases
Ensembl	ENSDART00000080461; ENSDARP00000074910; ENSDARG00000057721; Danio rerio. [Genome view]
GeneID	58051.
KEGG	dre:58051.
Organism-specific databases
CTD	58051.
ZFIN	ZDB-GENE-000823-5. hoxa1a.
Phylogenomic databases
HOGENOM	HBG717389.
HOVERGEN	Q98SI1.
InParanoid	Q98SI1.
OMA	VEAYSSN.
OrthoDB	EOG9GB9RJ.
Gene expression databases
ArrayExpress	Q98SI1.
Bgee	Q98SI1.
Family and domain databases
InterPro	IPR001356. Homeobox. IPR017970. Homeobox_CS. IPR020479. Homeobox_region. IPR009057. Homeodomain-like. IPR012287. Homeodomain-rel. [Graphical view]
Gene3D	G3DSA:1.10.10.60. Homeodomain-rel. 1 hit.
Pfam	PF00046. Homeobox. 1 hit. [Graphical view]
PRINTS	PR00024. HOMEOBOX.
SMART	SM00389. HOX. 1 hit. [Graphical view]
PROSITE	PS00032. ANTENNAPEDIA. False negative. PS00027. HOMEOBOX_1. 1 hit. PS50071. HOMEOBOX_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

HXA1A_DANRE

Accession

Primary (citable) accession number: Q98SI1
Secondary accession number(s): Q1L968 , Q4PRB2, Q8AWZ1, Q98SI0, Q9YGT8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 2005
Last sequence update:	June 1, 2001
Last modified:	December 15, 2009
This is version 49 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Zebrafish annotation project