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Database: UniProt
Entry: E9QD84_DANRE
LinkDB: E9QD84_DANRE
Original site: E9QD84_DANRE 
ID   E9QD84_DANRE            Unreviewed;       764 AA.
AC   E9QD84; A0A8N7UZF9;
DT   05-APR-2011, integrated into UniProtKB/TrEMBL.
DT   11-JUL-2012, sequence version 2.
DT   24-JAN-2024, entry version 75.
DE   SubName: Full=Semaphorin-3D {ECO:0000313|Ensembl:ENSDARP00000091966, ECO:0000313|RefSeq:NP_571123.2};
GN   Name=sema2 {ECO:0000313|RefSeq:NP_571123.2};
GN   Synonyms=semaZ2 {ECO:0000313|RefSeq:NP_571123.2};
GN   OrderedLocusNames=sema3d {ECO:0000313|Ensembl:ENSDARP00000091966,
GN   ECO:0000313|RefSeq:NP_571123.2, ECO:0000313|ZFIN:ZDB-GENE-990715-2};
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955 {ECO:0000313|Ensembl:ENSDARP00000091966};
RN   [1] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=10821754;
RA   Shanmugalingam S., Houart C., Picker A., Reifers F., Macdonald R.,
RA   Barth A., Griffin K., Brand M., Wilson S.W.;
RT   "Ace/Fgf8 is required for forebrain commissure formation and patterning of
RT   the telencephalon.";
RL   Development 127:2549-2561(2000).
RN   [2] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=14724229;
RA   Liu Y., Berndt J., Su F., Tawarayama H., Shoji W., Kuwada J.Y.,
RA   Halloran M.C.;
RT   "Semaphorin3D guides retinal axons along the dorsoventral axis of the
RT   tectum.";
RL   J. Neurosci. 24:310-318(2004).
RN   [3] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=15456815;
RA   Wolman M.A., Liu Y., Tawarayama H., Shoji W., Halloran M.C.;
RT   "Repulsion and attraction of axons by semaphorin3D are mediated by
RT   different neuropilins in vivo.";
RL   J. Neurosci. 24:8428-8435(2004).
RN   [4] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=15882579; DOI=10.1016/j.ydbio.2005.01.029;
RA   Yu H.H., Moens C.B.;
RT   "Semaphorin signaling guides cranial neural crest cell migration in
RT   zebrafish.";
RL   Dev. Biol. 280:373-385(2005).
RN   [5] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=16033800;
RA   Barresi M.J., Hutson L.D., Chien C.B., Karlstrom R.O.;
RT   "Hedgehog regulated Slit expression determines commissure and glial cell
RT   position in the zebrafish forebrain.";
RL   Development 132:3643-3656(2005).
RN   [6] {ECO:0000313|Ensembl:ENSDARP00000091966}
RP   IDENTIFICATION.
RC   STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000091966};
RG   Ensembl;
RL   Submitted (JUL-2011) to UniProtKB.
RN   [7] {ECO:0000313|Ensembl:ENSDARP00000091966, ECO:0000313|Proteomes:UP000000437}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000091966};
RX   PubMed=23594743; DOI=10.1038/nature12111;
RG   Genome Reference Consortium Zebrafish;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., 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., Elliot D., Eliott D.,
RA   Threadgold G., Harden G., Ware D., Begum S., Mortimore B., Mortimer B.,
RA   Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M.,
RA   Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M.,
RA   Glithero R., Howden P., Barker N., Lloyd C., Stevens C., Harley J.,
RA   Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D.,
RA   Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K.,
RA   Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R.,
RA   Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M.,
RA   Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D.,
RA   Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M.,
RA   Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M.,
RA   Woodmansey R., Clark G., Cooper J., Cooper J., Tromans A., Grafham D.,
RA   Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J.,
RA   Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I.,
RA   Berger A., 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., Lanz C., Raddatz G., Osoegawa K., Zhu B.,
RA   Rapp A., Widaa S., Langford C., Yang F., Schuster S.C., Carter N.P.,
RA   Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R.,
RA   Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I.,
RA   Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H.,
RA   Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [8] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=27799363;
RA   Hamm M.J., Kirchmaier B.C., Herzog W.;
RT   "Sema3d controls collective endothelial cell migration by distinct
RT   mechanisms via Nrp1 and PlxnD1.";
RL   J. Cell Biol. 215:415-430(2016).
RN   [9] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=29084713; DOI=10.1242/bio.026013;
RA   Banerji R., Skibbens R.V., Iovine M.K.;
RT   "Cohesin mediates Esco2-dependent transcriptional regulation in a zebrafish
RT   regenerating fin model of Roberts Syndrome.";
RL   Biol. Open 6:1802-1813(2017).
RN   [10] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=28448525;
RA   Miyake A., Mekata Y., Fujibayashi H., Nakanishi K., Konishi M., Itoh N.;
RT   "Brorin is required for neurogenesis, gliogenesis, and commissural axon
RT   guidance in the zebrafish forebrain.";
RL   PLoS ONE 12:e0176036-e0176036(2017).
RN   [11] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=30661757;
RG   INTERVAL;
RG   UK10K Consortium;
RA   van der Klaauw A.A., Croizier S., Mendes de Oliveira E., Stadler L.K.J.,
RA   Park S., Kong Y., Banton M.C., Tandon P., Hendricks A.E., Keogh J.M.,
RA   Riley S.E., Papadia S., Henning E., Bounds R., Bochukova E.G., Mistry V.,
RA   O'Rahilly S., Simerly R.B., Minchin J.E.N., Barroso I., Jones E.Y.,
RA   Bouret S.G., Farooqi I.S.;
RT   "Human Semaphorin 3 Variants Link Melanocortin Circuit Development and
RT   Energy Balance.";
RL   Cell 176:729-742(2019).
RN   [12] {ECO:0000313|RefSeq:NP_571123.2}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RX   PubMed=30695021;
RA   Turner K.J., Hoyle J., Valdivia L.E., Cerveny K.L., Hart W., Mangoli M.,
RA   Geisler R., Rees M., Houart C., Poole R.J., Wilson S.W., Gestri G.;
RT   "Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure
RT   of cells to transition from proliferation to differentiation, retinal
RT   coloboma and midline axon guidance deficits.";
RL   PLoS ONE 14:e0211073-e0211073(2019).
RN   [13] {ECO:0000313|RefSeq:NP_571123.2}
RP   IDENTIFICATION.
RC   STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_571123.2};
RG   RefSeq;
RL   Submitted (SEP-2023) to UniProtKB.
CC   -!- SIMILARITY: Belongs to the semaphorin family.
CC       {ECO:0000256|ARBA:ARBA00009492}.
CC   -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {ECO:0000256|PROSITE-ProRule:PRU00352}.
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DR   EMBL; CU633862; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CU855784; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CU861648; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   RefSeq; NP_571123.2; NM_131048.2.
DR   Ensembl; ENSDART00000101192; ENSDARP00000091966; ENSDARG00000017369.
DR   Ensembl; ENSDART00000101192.7; ENSDARP00000091966.5; ENSDARG00000017369.11.
DR   GeneID; 30250; -.
DR   KEGG; dre:30250; -.
DR   CTD; 223117; -.
DR   ZFIN; ZDB-GENE-990715-2; sema3d.
DR   HOGENOM; CLU_009051_5_0_1; -.
DR   OMA; KIYWPAT; -.
DR   OrthoDB; 5342713at2759; -.
DR   Proteomes; UP000000437; Chromosome 18.
DR   Bgee; ENSDARG00000017369; Expressed in pectoral fin and 68 other cell types or tissues.
DR   GO; GO:0030215; F:semaphorin receptor binding; IEA:InterPro.
DR   GO; GO:0007411; P:axon guidance; IEA:UniProt.
DR   CDD; cd05871; Ig_Sema3; 1.
DR   CDD; cd11252; Sema_3D; 1.
DR   Gene3D; 2.60.40.10; Immunoglobulins; 1.
DR   Gene3D; 3.30.1680.10; ligand-binding face of the semaphorins, domain 2; 1.
DR   Gene3D; 2.130.10.10; YVTN repeat-like/Quinoprotein amine dehydrogenase; 1.
DR   InterPro; IPR036179; Ig-like_dom_sf.
DR   InterPro; IPR013783; Ig-like_fold.
DR   InterPro; IPR016201; PSI.
DR   InterPro; IPR042582; Sema3D_Sema.
DR   InterPro; IPR001627; Semap_dom.
DR   InterPro; IPR036352; Semap_dom_sf.
DR   InterPro; IPR027231; Semaphorin.
DR   InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR   PANTHER; PTHR11036; SEMAPHORIN; 1.
DR   PANTHER; PTHR11036:SF36; SEMAPHORIN-3D; 1.
DR   Pfam; PF01403; Sema; 1.
DR   SMART; SM00423; PSI; 1.
DR   SMART; SM00630; Sema; 1.
DR   SUPFAM; SSF48726; Immunoglobulin; 1.
DR   SUPFAM; SSF103575; Plexin repeat; 1.
DR   SUPFAM; SSF101912; Sema domain; 1.
DR   PROSITE; PS51004; SEMA; 1.
PE   3: Inferred from homology;
KW   Disulfide bond {ECO:0000256|ARBA:ARBA00023157};
KW   Glycoprotein {ECO:0000256|ARBA:ARBA00023180};
KW   Reference proteome {ECO:0000313|Proteomes:UP000000437};
KW   Signal {ECO:0000313|RefSeq:NP_571123.2}.
FT   CHAIN           42..764
FT                   /note="Semaphorin-3D"
FT                   /evidence="ECO:0000313|RefSeq:NP_571123.2"
FT                   /id="PRO_5035036319"
FT   DOMAIN          48..535
FT                   /note="Sema"
FT                   /evidence="ECO:0000259|PROSITE:PS51004"
FT   REGION          743..764
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   764 AA;  87884 MW;  9DFFC304202699CA CRC64;
     MKTAGEPDRR RQRRQVRTGR FSCAWWSTSV MLFFSLPEGN CMKESLPRVK LGYKDLIHSR
     SVVPFTGSSE GQHFQTVLLD EERSRLLLGA KDHVYLLDPD NINKHPKKLS WPASRDRVEM
     CILAGKNPLT ECANFIRVLH SYNRTHVYAC GTGAFHPTCA FLEIKGHKED RWLQLHSNTM
     ESGRMKCPFD PNQPFASVLT DQYLYAGTAS DFLGKDSTFT RSLGPPPHQQ YIRTDISEDY
     WINEGKFISA HPISDTYNPD DDKIYFFFRE ASRDGSTTDK SVLSRVARIC RNDVGGLRSL
     TNKWTTFLKA RLVCSIPGPD GVDTHFDELQ DIFLLPSRDE KNPMVYGVFT TTSSIFKGSA
     VCVYTMEDIR AAFNGPYAHK EGPDHRWVEY EGRIPYPRPG TCPSRTYDPH IKTTKDFPDE
     VISFIRLHPL MYQSVHPMTG RPIFTRINTE YRLTQIIVDR VAAEDGQYAV MFLGTDMGSV
     LKVVSITQEN WSSEEIILEE LQVFKNPSPI LNMEVSSKQQ QLFVGGSDGL VQVSLHRCHI
     YGQGCAECCL ARDPYCAWDG TQCSRYIPAS KRRARRQDIK HGDPSSHCWD TEDVLGRNVE
     EKVLYGVESN SSFLECVSKS QQALIRWFVL KPGVDHRQEI KPDERVLITD RGLLIRWLQR
     GDAGSYFCTS QEHRFTRTLL HVSLHILDRG QINAHQPAIR ESSENPAVTE PRQRYKDYLR
     MLSGPARSLD EYCETMWHRE KKQKQKGKWK HVQELRKSRN RRHH
//
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