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Q9DE25

- FXC1A_DANRE

UniProt

Q9DE25 - FXC1A_DANRE

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Protein

Forkhead box C1-A

Gene

foxc1a

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

Functioni

Transcriptional regulator. Required for cell viability and resistance to oxidative stress in the eye through regulation of FOXO1A.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi74 – 16895Fork-headPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. chromatin DNA binding Source: RefGenome
  2. DNA binding, bending Source: RefGenome
  3. double-stranded DNA binding Source: RefGenome
  4. RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity Source: RefGenome
  5. sequence-specific DNA binding Source: InterPro
  6. transcription factor binding Source: RefGenome

GO - Biological processi

  1. adrenal gland development Source: ZFIN
  2. blood vessel development Source: ZFIN
  3. camera-type eye development Source: ZFIN
  4. closure of optic fissure Source: ZFIN
  5. glomerular visceral epithelial cell fate commitment Source: ZFIN
  6. negative regulation of apoptotic process Source: RefGenome
  7. negative regulation of transcription from RNA polymerase II promoter Source: RefGenome
  8. Notch signaling pathway Source: RefGenome
  9. positive regulation of transcription from RNA polymerase II promoter Source: RefGenome
  10. pronephric glomerulus development Source: ZFIN
  11. regulation of organ growth Source: RefGenome
  12. regulation of sequence-specific DNA binding transcription factor activity Source: RefGenome
  13. regulation of vascular permeability Source: ZFIN
  14. somitogenesis Source: ZFIN
  15. transcription from RNA polymerase II promoter Source: GOC
  16. vascular endothelial growth factor receptor signaling pathway Source: RefGenome
  17. vasculature development Source: ZFIN
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Forkhead box C1-A
Gene namesi
Name:foxc1a
Synonyms:foxc1.1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Chromosome 2

Organism-specific databases

ZFINiZDB-GENE-010302-1. foxc1a.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
  2. transcription factor complex Source: RefGenome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 476476Forkhead box C1-APRO_0000419248Add
BLAST

Proteomic databases

PRIDEiQ9DE25.

Expressioni

Developmental stagei

First detected at the shield stage of gastrulation in the involuting mesendoderm with levels being highest in the paraxial mesoderm and decline laterally to become undetectable in the ventral mesoderm. Expression spreads in the hypoblast towards the animal pole and converges dorsally. At the tail bud stage (9.5 hpf), transcripts are seen in adaxial cells flanking the future notochord and in the presomitic mesoderm (PSM). During early somitogenesis, expression also extends into the future head, in two stripes continuous with the adaxial cells. Expression continues around the developing eye, presomitic mesoderm (PSM), trunk adaxial cells and somites. In late somatogenesis, expression in the presumptive pronephric primodia lateral to the second and third somite. In the early pharyngula stage, expressed in the perioptic mesoderm. Expression continues in the PSM and adaxial cells in the tail.1 Publication

Gene expression databases

BgeeiQ9DE25.

Structurei

3D structure databases

ProteinModelPortaliQ9DE25.
SMRiQ9DE25. Positions 72-164.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi239 – 33799Ser-richAdd
BLAST
Compositional biasi377 – 3804Poly-Thr

Sequence similaritiesi

Contains 1 fork-head DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00760000118904.
HOGENOMiHOG000007939.
HOVERGENiHBG051640.
InParanoidiQ9DE25.
KOiK09396.
OMAiYSSPCSQ.
OrthoDBiEOG7C8GHD.
PhylomeDBiQ9DE25.
TreeFamiTF316127.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR001766. TF_fork_head.
IPR018122. TF_fork_head_CS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00250. Fork_head. 1 hit.
[Graphical view]
PRINTSiPR00053. FORKHEAD.
SMARTiSM00339. FH. 1 hit.
[Graphical view]
PROSITEiPS00657. FORK_HEAD_1. 1 hit.
PS00658. FORK_HEAD_2. 1 hit.
PS50039. FORK_HEAD_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9DE25-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQARYSVSSP NSLGVVPYIS SDQSYYRAAA GGGYTGMPAP MTMYSHAAHD
60 70 80 90 100
QYPASMARAY GPYTPQPQPK DMVKPPYSYI ALITMAIQNS PDKKVTLNGI
110 120 130 140 150
YQFIMERFPF YRDNKQGWQN SIRHNLSLNE CFVKVPRDDK KPGKGSYWTL
160 170 180 190 200
DPDSYNMFEN GSFLRRRRRF KKKDAMKDKE DRGVKEAPSR QAQPQAREQE
210 220 230 240 250
QSVPGSQPVR IQDIKTENGT STPPQAVSPT LSTVPKIESP DSSSSMSSGS
260 270 280 290 300
PHSIPSTRSL SLDSAGEQHH QAPAQGFSVD NIMTSLRGSP HSSGELTPSL
310 320 330 340 350
VAPSRTGITP TLSLNYSPNQ SSVYSSPCSQ NSISTTSNAT YHCNMQAMSL
360 370 380 390 400
YAGGDRSGHL GTTATTVDET LPDYSITTTT SSLSHGNLSS AQEGHHPHQG
410 420 430 440 450
RLASWYLNQA GDIGHLGATY PAQQQNFHSV REMFESQRIG LNNSPVNGNN
460 470
SCQMSFPPSQ PIYRTSGAFV YDCSKF
Length:476
Mass (Da):52,173
Last modified:March 1, 2001 - v1
Checksum:iE79BD7030D20B2D0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU929125 Genomic DNA. No translation available.
AF219949 Genomic DNA. Translation: AAG44241.1.
BC053129 mRNA. Translation: AAH53129.1.
RefSeqiNP_571803.1. NM_131728.3.
UniGeneiDr.82483.

Genome annotation databases

EnsembliENSDART00000122732; ENSDARP00000105372; ENSDARG00000091481.
GeneIDi100148408.
KEGGidre:100148408.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU929125 Genomic DNA. No translation available.
AF219949 Genomic DNA. Translation: AAG44241.1 .
BC053129 mRNA. Translation: AAH53129.1 .
RefSeqi NP_571803.1. NM_131728.3.
UniGenei Dr.82483.

3D structure databases

ProteinModelPortali Q9DE25.
SMRi Q9DE25. Positions 72-164.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi Q9DE25.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSDART00000122732 ; ENSDARP00000105372 ; ENSDARG00000091481 .
GeneIDi 100148408.
KEGGi dre:100148408.

Organism-specific databases

CTDi 100148408.
ZFINi ZDB-GENE-010302-1. foxc1a.

Phylogenomic databases

GeneTreei ENSGT00760000118904.
HOGENOMi HOG000007939.
HOVERGENi HBG051640.
InParanoidi Q9DE25.
KOi K09396.
OMAi YSSPCSQ.
OrthoDBi EOG7C8GHD.
PhylomeDBi Q9DE25.
TreeFami TF316127.

Miscellaneous databases

NextBioi 20792036.

Gene expression databases

Bgeei Q9DE25.

Family and domain databases

Gene3Di 1.10.10.10. 1 hit.
InterProi IPR001766. TF_fork_head.
IPR018122. TF_fork_head_CS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami PF00250. Fork_head. 1 hit.
[Graphical view ]
PRINTSi PR00053. FORKHEAD.
SMARTi SM00339. FH. 1 hit.
[Graphical view ]
PROSITEi PS00657. FORK_HEAD_1. 1 hit.
PS00658. FORK_HEAD_2. 1 hit.
PS50039. FORK_HEAD_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and expression of zebrafish foxc1a and foxc1b, encoding conserved forkhead/winged helix transcription factors."
    Topczewska J.M., Topczewski J., Solnica-Krezel L., Hogan B.L.
    Mech. Dev. 100:343-347(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DEVELOPMENTAL STAGE.
  2. "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.
  3. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.

Entry informationi

Entry nameiFXC1A_DANRE
AccessioniPrimary (citable) accession number: Q9DE25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: March 1, 2001
Last modified: October 29, 2014
This is version 109 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3