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
//