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Protein

Paired box protein Pax-2a

Gene

pax2a

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

Functioni

Probable transcription factor involved in the development of the midbrain/hindbrain boundary (MHB) organizer and specification of neuronal cell fates. Required for establishment of eng2 and eng3 gene expression in the midbrain and MHB primordium during late gastrulation.1 Publication

GO - Molecular functioni

  • DNA binding Source: UniProtKB
  • sequence-specific DNA binding Source: ZFIN
  • transcription factor activity, sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • anterior/posterior pattern specification Source: ZFIN
  • anterior/posterior pattern specification involved in pronephros development Source: ZFIN
  • cell fate specification Source: ZFIN
  • cerebellum development Source: ZFIN
  • cerebellum formation Source: ZFIN
  • embryonic camera-type eye morphogenesis Source: ZFIN
  • embryonic pattern specification Source: ZFIN
  • hindbrain development Source: ZFIN
  • inner ear receptor cell differentiation Source: ZFIN
  • kidney development Source: ZFIN
  • locus ceruleus development Source: ZFIN
  • midbrain development Source: ZFIN
  • midbrain-hindbrain boundary development Source: ZFIN
  • nervous system development Source: UniProtKB
  • otic placode formation Source: ZFIN
  • peripheral nervous system development Source: ZFIN
  • pronephric glomerulus morphogenesis Source: ZFIN
  • pronephros development Source: ZFIN
  • pronephros morphogenesis Source: ZFIN
  • thyroid gland development Source: ZFIN
  • transcription, DNA-templated Source: UniProtKB-KW
  • vestibular receptor cell development Source: ZFIN
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Paired box protein Pax-2a
Alternative name(s):
No isthmus protein
Pax[Zf-b]
Gene namesi
Name:pax2a
Synonyms:noi, pax2.1, paxzf-b
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 13

Organism-specific databases

ZFINiZDB-GENE-990415-8. pax2a.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: ZFIN
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 410410Paired box protein Pax-2aPRO_0000050177Add
BLAST

Proteomic databases

PaxDbiQ90268.

Expressioni

Tissue specificityi

Expressed during embryogenesis in the kidney, optic stalk, midbrain, otic vesicle and a row of cells along the spinal cord and the hindbrain.

Developmental stagei

First seen during the formation of neural keel. At 9-10 hours of development expression seen in two laterally located transverse stripes of cells in the rostral 1/3 of the embryo, and the two areas subsequently move towards the midline and form the posterior portion of the midbrain. Detected in the otic placode, Wolffian duct including the nephritic primordium and optic stalk at 10-12 hours. At 14-15 hours expression seen in the single cells along the spinal cord, presumably interneurons.

Gene expression databases

BgeeiQ90268.
ExpressionAtlasiQ90268. differential.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000071460.

Structurei

3D structure databases

ProteinModelPortaliQ90268.
SMRiQ90268. Positions 22-145.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini19 – 145127PairedPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 paired domain.PROSITE-ProRule annotation

Keywords - Domaini

Paired box

Phylogenomic databases

eggNOGiKOG3862. Eukaryota.
ENOG410ZT0S. LUCA.
GeneTreeiENSGT00680000099553.
HOVERGENiHBG009115.
InParanoidiQ90268.
KOiK15608.
OrthoDBiEOG7WT431.
PhylomeDBiQ90268.
TreeFamiTF315397.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
InterProiIPR009057. Homeodomain-like.
IPR001523. Paired_dom.
IPR022130. Pax2_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00292. PAX. 1 hit.
PF12403. Pax2_C. 1 hit.
[Graphical view]
PRINTSiPR00027. PAIREDBOX.
SMARTiSM00351. PAX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00034. PAIRED_1. 1 hit.
PS51057. PAIRED_2. 1 hit.
[Graphical view]

Sequences (12)i

Sequence statusi: Complete.

This entry describes 12 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.

Isoform 4 (identifier: Q90268-1) [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
MDIHCKADPF SAMHLSHIGH GGVNQLGGVF VNGRPLPDVV RQRIVELAHQ
60 70 80 90 100
GVRPCDISRQ LRVSHGCVSK ILGRYYETGS IKPGVIGGSK PKVATPKVVE
110 120 130 140 150
KIAEYKRQNP TMFAWEIRDR LLAEGVCDND TVPSVSSINR IIRTKVQQPF
160 170 180 190 200
HPSSDGTGTP LSTAGHTIVP STASPPVSSA SNDPVGSYSI NGILGIPRSN
210 220 230 240 250
GEKRKRDDVL WSGNHLDGRK IGYHGSDGSG PNSDSQGSVE SLRKHLRADA
260 270 280 290 300
FTQQQLEALD RVFERPSYPD VFPTSEHIKP EQANEYSLPA LNPGLDEVKP
310 320 330 340 350
SLSTSVSSDL GSSVSQSYPV VTGREMASTT LPGYPPHVPP TGQGSYPTST
360 370 380 390 400
LAGMVPGSDF SGNPYSHPQY TTYNEAWRFS NPALLSSPYY YSAASRGSGP
410
PTAATAYDRH
Length:410
Mass (Da):44,099
Last modified:May 27, 2002 - v2
Checksum:i6BE302826C516FD7
GO
Isoform 1 (identifier: Q90268-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R

Show »
Length:406
Mass (Da):43,748
Checksum:i5FA7AE607B8459AA
GO
Isoform 2 (identifier: Q90268-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R
     209-224: VLWSGNHLDGRKIGYH → D

Show »
Length:391
Mass (Da):42,029
Checksum:i945AA4986AE92EDB
GO
Isoform 3 (identifier: Q90268-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     323-334: GREMASTTLPGY → DKSAGSTVPAGH
     335-410: Missing.

Show »
Length:334
Mass (Da):35,851
Checksum:i2BBDAFFEFD23FADA
GO
Isoform 5 (identifier: Q90268-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R
     209-224: VLWSGNHLDGRKIGYH → D
     283-322: Missing.

Show »
Length:351
Mass (Da):37,950
Checksum:i8832D34E75D5F0E0
GO
Isoform 6 (identifier: Q90268-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R
     209-322: Missing.

Show »
Length:292
Mass (Da):31,410
Checksum:i3D86C3147EEBD30A
GO
Isoform 7 (identifier: Q90268-7) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R
     323-334: GREMASTTLPGY → DKSAGSTVPAGH
     335-410: Missing.

Show »
Length:330
Mass (Da):35,500
Checksum:i122C55AA129118F8
GO
Isoform 8 (identifier: Q90268-8) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     386-410: SSPYYYSAASRGSGPPTAATAYDRH → MPHPGAPGLPLLPLPMTAT

Show »
Length:404
Mass (Da):43,377
Checksum:i6EDC36E73C32675F
GO
Isoform 9 (identifier: Q90268-9) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     209-224: VLWSGNHLDGRKIGYH → D
     386-410: SSPYYYSAASRGSGPPTAATAYDRH → MPHPGAPGLPLLPLPMTAT

Show »
Length:389
Mass (Da):41,658
Checksum:i37B68840DF11B472
GO
Isoform 10 (identifier: Q90268-10) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R
     209-224: VLWSGNHLDGRKIGYH → D
     386-410: SSPYYYSAASRGSGPPTAATAYDRH → MPHPGAPGLPLLPLPMTAT

Show »
Length:385
Mass (Da):41,306
Checksum:i2FD08B99DB3FD5DF
GO
Isoform 11 (identifier: Q90268-11) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     15-19: LSHIG → R
     386-410: SSPYYYSAASRGSGPPTAATAYDRH → MPHPGAPGLPLLPLPMTAT

Show »
Length:400
Mass (Da):43,025
Checksum:iC8A1151F0D5C4610
GO
Isoform 12 (identifier: Q90268-12) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     209-224: VLWSGNHLDGRKIGYH → D

Show »
Length:395
Mass (Da):42,380
Checksum:i9629926611BDC6BD
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti74 – 796Missing in allele TM243A; no midbrain/hindbrain boundary.
Natural varianti79 – 791G → V in allele TY31A; no midbrain/hindbrain boundary.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei15 – 195LSHIG → R in isoform 1, isoform 2, isoform 5, isoform 6, isoform 7, isoform 10 and isoform 11. 2 PublicationsVSP_002348
Alternative sequencei209 – 322114Missing in isoform 6. CuratedVSP_002350Add
BLAST
Alternative sequencei209 – 22416VLWSG…KIGYH → D in isoform 2, isoform 5, isoform 9, isoform 10 and isoform 12. 1 PublicationVSP_002349Add
BLAST
Alternative sequencei283 – 32240Missing in isoform 5. CuratedVSP_002351Add
BLAST
Alternative sequencei323 – 33412GREMA…TLPGY → DKSAGSTVPAGH in isoform 3 and isoform 7. CuratedVSP_002352Add
BLAST
Alternative sequencei335 – 41076Missing in isoform 3 and isoform 7. CuratedVSP_002353Add
BLAST
Alternative sequencei386 – 41025SSPYY…AYDRH → MPHPGAPGLPLLPLPMTAT in isoform 8, isoform 9, isoform 10 and isoform 11. CuratedVSP_002354Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63961 mRNA. Translation: CAA45378.1.
AF067530 mRNA. Translation: AAD19285.1.
AF067531 mRNA. Translation: AAD19286.1.
AF067532 mRNA. Translation: AAD19287.1.
AF067533 mRNA. Translation: AAD19288.1.
AF067534 mRNA. Translation: AAD19289.1.
AF067535 mRNA. Translation: AAD19290.1.
AF067536 mRNA. Translation: AAD19291.1.
AF067537 mRNA. Translation: AAD19292.1.
AF067538 mRNA. Translation: AAD19293.1.
AF067539 mRNA. Translation: AAD19294.1.
AF067540 mRNA. Translation: AAD19295.1.
AF067541 mRNA. Translation: AAD19296.1.
BC066690 mRNA. Translation: AAH66690.1.
PIRiS23341.
RefSeqiNP_571259.1. NM_131184.2. [Q90268-3]
XP_005156806.1. XM_005156749.2. [Q90268-12]
UniGeneiDr.75076.

Genome annotation databases

EnsembliENSDART00000076998; ENSDARP00000071466; ENSDARG00000028148. [Q90268-3]
ENSDART00000134424; ENSDARP00000121417; ENSDARG00000028148. [Q90268-6]
GeneIDi30425.
KEGGidre:30425.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63961 mRNA. Translation: CAA45378.1.
AF067530 mRNA. Translation: AAD19285.1.
AF067531 mRNA. Translation: AAD19286.1.
AF067532 mRNA. Translation: AAD19287.1.
AF067533 mRNA. Translation: AAD19288.1.
AF067534 mRNA. Translation: AAD19289.1.
AF067535 mRNA. Translation: AAD19290.1.
AF067536 mRNA. Translation: AAD19291.1.
AF067537 mRNA. Translation: AAD19292.1.
AF067538 mRNA. Translation: AAD19293.1.
AF067539 mRNA. Translation: AAD19294.1.
AF067540 mRNA. Translation: AAD19295.1.
AF067541 mRNA. Translation: AAD19296.1.
BC066690 mRNA. Translation: AAH66690.1.
PIRiS23341.
RefSeqiNP_571259.1. NM_131184.2. [Q90268-3]
XP_005156806.1. XM_005156749.2. [Q90268-12]
UniGeneiDr.75076.

3D structure databases

ProteinModelPortaliQ90268.
SMRiQ90268. Positions 22-145.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000071460.

Proteomic databases

PaxDbiQ90268.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000076998; ENSDARP00000071466; ENSDARG00000028148. [Q90268-3]
ENSDART00000134424; ENSDARP00000121417; ENSDARG00000028148. [Q90268-6]
GeneIDi30425.
KEGGidre:30425.

Organism-specific databases

CTDi30425.
ZFINiZDB-GENE-990415-8. pax2a.

Phylogenomic databases

eggNOGiKOG3862. Eukaryota.
ENOG410ZT0S. LUCA.
GeneTreeiENSGT00680000099553.
HOVERGENiHBG009115.
InParanoidiQ90268.
KOiK15608.
OrthoDBiEOG7WT431.
PhylomeDBiQ90268.
TreeFamiTF315397.

Miscellaneous databases

PROiQ90268.

Gene expression databases

BgeeiQ90268.
ExpressionAtlasiQ90268. differential.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
InterProiIPR009057. Homeodomain-like.
IPR001523. Paired_dom.
IPR022130. Pax2_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00292. PAX. 1 hit.
PF12403. Pax2_C. 1 hit.
[Graphical view]
PRINTSiPR00027. PAIREDBOX.
SMARTiSM00351. PAX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00034. PAIRED_1. 1 hit.
PS51057. PAIRED_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Expression of the zebrafish paired box gene pax[zf-b] during early neurogenesis."
    Krauss S., Johansen T., Korzh V., Fjose A.
    Development 113:1193-1206(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
    Strain: NC-1.
    Tissue: Embryo.
  2. "A series of no isthmus (noi) alleles of the zebrafish pax2.1 gene reveals multiple signaling events in development of the midbrain-hindbrain boundary."
    Lun K., Brand M.
    Development 125:3049-3062(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], ALTERNATIVE SPLICING, VARIANTS, FUNCTION.
    Strain: Tuebingen.
    Tissue: Embryo.
  3. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (MAR-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Kidney.

Entry informationi

Entry nameiPAX2A_DANRE
AccessioniPrimary (citable) accession number: Q90268
Secondary accession number(s): Q9PWK8
, Q9PWK9, Q9PWL0, Q9PWL1, Q9YGU5, Q9YGU6, Q9YGU7, Q9YGU8, Q9YGU9, Q9YGV0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: May 27, 2002
Last modified: June 8, 2016
This is version 125 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. 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.