ID FOXN4_DANRE Reviewed; 550 AA.
AC A2BGM5; Q8UVH2; Q90X68; Q9DG30; Q9PT94;
DT 14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
DT 20-FEB-2007, sequence version 1.
DT 29-OCT-2014, entry version 66.
DE RecName: Full=Forkhead box protein N4;
GN Name=foxn4; Synonyms=sli, slipjig;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Cyprinidae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=11054532; DOI=10.1016/S0378-1119(00)00344-9;
RA Schlake T., Schorpp M., Boehm T.;
RT "Formation of regulator/target gene relationships during evolution.";
RL Gene 256:29-34(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), DEVELOPMENTAL STAGE,
RP AND TISSUE SPECIFICITY.
RC STRAIN=Tuebingen; TISSUE=Thymus;
RX PubMed=15464224; DOI=10.1016/j.devbrainres.2004.05.014;
RA Danilova N., Visel A., Willett C.E., Steiner L.A.;
RT "Expression of the winged helix/forkhead gene, foxn4, during zebrafish
RT development.";
RL Brain Res. Dev. Brain Res. 153:115-119(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C.,
RA Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L.,
RA McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C.,
RA Koch R., Rauch G.J., White S., Chow W., Kilian B., Quintais L.T.,
RA Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T.,
RA Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F.,
RA Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H.,
RA Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G.,
RA Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B.,
RA Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S.,
RA Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C.,
RA Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H.,
RA Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C.,
RA Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J.,
RA Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S.,
RA Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R.,
RA Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R.,
RA Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R.,
RA Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A.,
RA Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
RA Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
RA Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S.,
RA Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J.,
RA Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C.,
RA Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H.,
RA Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J.,
RA Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the
RT human genome.";
RL Nature 496:498-503(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION IN HEART DEVELOPMENT, DISRUPTION PHENOTYPE, AND DNA-BINDING.
RX PubMed=18347092; DOI=10.1101/gad.1629408;
RA Chi N.C., Shaw R.M., De Val S., Kang G., Jan L.Y., Black B.L.,
RA Stainier D.Y.;
RT "Foxn4 directly regulates tbx2b expression and atrioventricular canal
RT formation.";
RL Genes Dev. 22:734-739(2008).
CC -!- FUNCTION: Transcription factor essential for neural and some non-
CC neural tissues development. Binds to an 11-bp consensus sequence
CC containing the invariant tetranucleotide 5'-ACGC-3'. During
CC development of the central nervous system, required to specify the
CC amacrine and horizontal cell fates from multipotent retinal
CC progenitors while suppressing the alternative photoreceptor cell
CC fates. Drives commitment of p2 progenitors to the V2b interneuron
CC fates during spinal cord neurogenesis. In development of non-
CC neural tissues, plays an essential role in the specification of
CC the atrioventricular canal. {ECO:0000269|PubMed:18347092}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
CC ProRule:PRU00089}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage; Named isoforms=3;
CC Name=1;
CC IsoId=A2BGM5-1; Sequence=Displayed;
CC Name=2;
CC IsoId=A2BGM5-2; Sequence=VSP_054327;
CC Name=3;
CC IsoId=A2BGM5-3; Sequence=VSP_054326;
CC -!- TISSUE SPECIFICITY: Isoform 1 is expressed mainly in adult thymus.
CC Isoform 2 is detected in adult skin. Isoform 3 is expressed in
CC adult brain and embryo. Prominent expression sites include the
CC olfactory placode, the basal layer of the olfactory epithelium,
CC the neuroepithelium of the developing retina, the germinal zone of
CC the differentiated eye, regions of motoneuron development in the
CC neural tube and periventricular regions of the brain.
CC {ECO:0000269|PubMed:15464224}.
CC -!- DEVELOPMENTAL STAGE: In embryo, expressed ubiquitously, but with
CC decreasing intensity, from the one-cell through gastrula stages.
CC {ECO:0000269|PubMed:15464224}.
CC -!- DISRUPTION PHENOTYPE: At 36-48 hpf, mutants exhibit pericardial
CC edema due to dysmorphic hearts that fail to loop and form and
CC atrioventricular (AV) canal. Hearts show continues peristatic
CC pumping rather than coordinated and sequential beating of atrial
CC and ventricular chambers. Endocardial cells remain squamous and AV
CC myocardial cell shape fail to occur.
CC {ECO:0000269|PubMed:18347092}.
CC -!- SIMILARITY: Contains 1 fork-head DNA-binding domain.
CC {ECO:0000255|PROSITE-ProRule:PRU00089}.
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DR EMBL; AJ252024; CAB64948.1; -; mRNA.
DR EMBL; AF198446; AAG27086.2; -; mRNA.
DR EMBL; AF424786; AAL17865.1; -; mRNA.
DR EMBL; AF443870; AAL38028.1; -; mRNA.
DR EMBL; BX510366; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BX510917; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC128811; AAI28812.1; -; mRNA.
DR RefSeq; NP_571174.1; NM_131099.2.
DR RefSeq; XP_005165156.1; XM_005165099.1. [A2BGM5-1]
DR UniGene; Dr.81266; -.
DR ProteinModelPortal; A2BGM5; -.
DR Ensembl; ENSDART00000008994; ENSDARP00000020367; ENSDARG00000010591. [A2BGM5-1]
DR GeneID; 30315; -.
DR KEGG; dre:30315; -.
DR CTD; 121643; -.
DR ZFIN; ZDB-GENE-990415-277; foxn4.
DR eggNOG; COG5025; -.
DR GeneTree; ENSGT00760000118794; -.
DR HOGENOM; HOG000232153; -.
DR HOVERGEN; HBG051655; -.
DR InParanoid; A2BGM5; -.
DR KO; K09407; -.
DR OMA; PSPQEYR; -.
DR OrthoDB; EOG77T146; -.
DR TreeFam; TF329867; -.
DR NextBio; 20806754; -.
DR PRO; PR:A2BGM5; -.
DR Bgee; Q90X68; -.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005667; C:transcription factor complex; IBA:RefGenome.
DR GO; GO:0003682; F:chromatin binding; ISS:UniProtKB.
DR GO; GO:0008301; F:DNA binding, bending; IBA:RefGenome.
DR GO; GO:0003690; F:double-stranded DNA binding; IBA:RefGenome.
DR GO; GO:0001158; F:enhancer sequence-specific DNA binding; ISS:UniProtKB.
DR GO; GO:0003705; F:RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity; IBA:RefGenome.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:ZFIN.
DR GO; GO:0003700; F:sequence-specific DNA binding transcription factor activity; ISS:UniProtKB.
DR GO; GO:0008134; F:transcription factor binding; IBA:RefGenome.
DR GO; GO:0035881; P:amacrine cell differentiation; ISS:UniProtKB.
DR GO; GO:0036302; P:atrioventricular canal development; IMP:UniProtKB.
DR GO; GO:0001947; P:heart looping; IMP:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IBA:RefGenome.
DR GO; GO:0048513; P:organ development; IBA:RefGenome.
DR GO; GO:0007389; P:pattern specification process; IBA:RefGenome.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0008016; P:regulation of heart contraction; IMP:UniProtKB.
DR GO; GO:0051090; P:regulation of sequence-specific DNA binding transcription factor activity; IBA:RefGenome.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0010842; P:retina layer formation; ISS:UniProtKB.
DR GO; GO:0009888; P:tissue development; IBA:RefGenome.
DR GO; GO:0006366; P:transcription from RNA polymerase II promoter; IBA:GOC.
DR GO; GO:0060579; P:ventral spinal cord interneuron fate commitment; ISS:UniProtKB.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR001766; TF_fork_head.
DR InterPro; IPR018122; TF_fork_head_CS.
DR InterPro; IPR011991; WHTH_DNA-bd_dom.
DR Pfam; PF00250; Fork_head; 1.
DR PRINTS; PR00053; FORKHEAD.
DR SMART; SM00339; FH; 1.
DR PROSITE; PS00658; FORK_HEAD_2; 1.
DR PROSITE; PS50039; FORK_HEAD_3; 1.
PE 1: Evidence at protein level;
KW Alternative promoter usage; Complete proteome; Developmental protein;
KW DNA-binding; Neurogenesis; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1 550 Forkhead box protein N4.
FT /FTId=PRO_0000428907.
FT DNA_BIND 231 327 Fork-head. {ECO:0000255|PROSITE-
FT ProRule:PRU00089}.
FT VAR_SEQ 1 139 Missing (in isoform 3).
FT {ECO:0000303|PubMed:15464224}.
FT /FTId=VSP_054326.
FT VAR_SEQ 1 134 MTVQSKLQGRGKFKKRFFRAGQQVPRPTLELSSVWLSKIFY
FT NPEQHHNKQKMIESGITTRMSGIHENPGQSHHTSAQDYRLL
FT TTDPSQLKDELPGDLQSLSWLTSVDVPRLQQIGGGRPDFTS
FT SAQSSLLERQT -> MAP (in isoform 2).
FT {ECO:0000303|PubMed:15464224}.
FT /FTId=VSP_054327.
FT CONFLICT 8 8 Q -> H (in Ref. 1; CAB64948, 2; AAG27086
FT and 4; AAI28812). {ECO:0000305}.
FT CONFLICT 39 39 I -> V (in Ref. 1; CAB64948).
FT {ECO:0000305}.
SQ SEQUENCE 550 AA; 60968 MW; D030E6C2022B33C0 CRC64;
MTVQSKLQGR GKFKKRFFRA GQQVPRPTLE LSSVWLSKIF YNPEQHHNKQ KMIESGITTR
MSGIHENPGQ SHHTSAQDYR LLTTDPSQLK DELPGDLQSL SWLTSVDVPR LQQIGGGRPD
FTSSAQSSLL ERQTAQLNSM TVAGGAGSAI HLQSEMQHSP LAINSMPQFS PGFPCAASVY
QTAPQQVLTF TQANQQCSPG GLYGNYNSQN LFPQPRITAH SQDLQPKCFP KPIYSYSCLI
AMALKNSKTG SLPVSEIYSF MKEHFPYFKT APDGWKNSVR HNLSLNKCFE KVENKMSGSS
RKGCLWALNP AKIDKMEEEM QKWKRKDLPA IRRSMANPDE LDKLITDRPE SCRQKSVDPG
MTRLPSCPPG QTLPLAAQMQ PQPVVTLSLQ CLPMHQHLQL QLQNQSRLAP SSPAPAQTPP
LHTVPDMTNS SLPQHPAKQH TDFYTVHTDV NSEVDALDPS IMDFAWQGNL WEEMKDDSFN
LEALGTLSNS PLRLSDCDLD TSSVTPVSSA GGLPYPDLQV TGLYSSYSAI DALSNQYMNT
QGGTKPIVLL
//