SEM3D_HUMAN
ID SEM3D_HUMAN Reviewed; 777 AA.
AC O95025; A6NK46; Q6UW77; Q8NCQ1;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Semaphorin-3D;
DE Flags: Precursor;
GN Name=SEMA3D; ORFNames=UNQ760/PRO1491;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT GLN-701.
RX PubMed=12975309; DOI=10.1101/gr.1293003;
RA Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J.,
RA Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P.,
RA Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E., Heldens S., Huang A.,
RA Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D.,
RA Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L.,
RA Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C.,
RA Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J.,
RA Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.;
RT "The secreted protein discovery initiative (SPDI), a large-scale effort to
RT identify novel human secreted and transmembrane proteins: a bioinformatics
RT assessment.";
RL Genome Res. 13:2265-2270(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=12853948; DOI=10.1038/nature01782;
RA Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H.,
RA Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K.,
RA Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A.,
RA Delehaunty K.D., Miner T.L., Nash W.E., Cordes M., Du H., Sun H.,
RA Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A.,
RA Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P.,
RA Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M.,
RA Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S.,
RA Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R.,
RA Strowmatt C., Latreille P., Miller N., Johnson D., Murray J.,
RA Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W.,
RA Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E.,
RA Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A.,
RA Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E.,
RA Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E.,
RA Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A.,
RA Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A.,
RA Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R.,
RA McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H.,
RA Wilson R.K.;
RT "The DNA sequence of human chromosome 7.";
RL Nature 424:157-164(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 327-777.
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: Induces the collapse and paralysis of neuronal growth cones.
CC Could potentially act as repulsive cues toward specific neuronal
CC populations. Binds to neuropilin (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000250}.
CC -!- DOMAIN: Strong binding to neuropilin is mediated by the carboxy third
CC of the protein.
CC -!- SIMILARITY: Belongs to the semaphorin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH29590.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AY358937; AAQ89296.1; -; mRNA.
DR EMBL; AC004957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC029590; AAH29590.1; ALT_INIT; mRNA.
DR CCDS; CCDS34676.1; -.
DR RefSeq; NP_689967.2; NM_152754.2.
DR RefSeq; XP_011514262.1; XM_011515960.1.
DR RefSeq; XP_016867362.1; XM_017011873.1.
DR AlphaFoldDB; O95025; -.
DR SMR; O95025; -.
DR BioGRID; 128826; 6.
DR IntAct; O95025; 1.
DR STRING; 9606.ENSP00000284136; -.
DR GlyGen; O95025; 3 sites.
DR iPTMnet; O95025; -.
DR PhosphoSitePlus; O95025; -.
DR BioMuta; SEMA3D; -.
DR EPD; O95025; -.
DR jPOST; O95025; -.
DR MassIVE; O95025; -.
DR PaxDb; O95025; -.
DR PeptideAtlas; O95025; -.
DR PRIDE; O95025; -.
DR ProteomicsDB; 50626; -.
DR Antibodypedia; 29622; 148 antibodies from 21 providers.
DR DNASU; 223117; -.
DR Ensembl; ENST00000284136.11; ENSP00000284136.6; ENSG00000153993.14.
DR GeneID; 223117; -.
DR KEGG; hsa:223117; -.
DR MANE-Select; ENST00000284136.11; ENSP00000284136.6; NM_001384900.1; NP_001371829.1.
DR UCSC; uc003uic.4; human.
DR CTD; 223117; -.
DR DisGeNET; 223117; -.
DR GeneCards; SEMA3D; -.
DR HGNC; HGNC:10726; SEMA3D.
DR HPA; ENSG00000153993; Group enriched (lymphoid tissue, thyroid gland).
DR MalaCards; SEMA3D; -.
DR MIM; 609907; gene.
DR neXtProt; NX_O95025; -.
DR OpenTargets; ENSG00000153993; -.
DR Orphanet; 388; Hirschsprung disease.
DR PharmGKB; PA35648; -.
DR VEuPathDB; HostDB:ENSG00000153993; -.
DR eggNOG; KOG3611; Eukaryota.
DR GeneTree; ENSGT00940000156681; -.
DR HOGENOM; CLU_009051_5_0_1; -.
DR InParanoid; O95025; -.
DR OMA; QDHHYIR; -.
DR OrthoDB; 297290at2759; -.
DR PhylomeDB; O95025; -.
DR TreeFam; TF316102; -.
DR PathwayCommons; O95025; -.
DR SignaLink; O95025; -.
DR BioGRID-ORCS; 223117; 8 hits in 1065 CRISPR screens.
DR ChiTaRS; SEMA3D; human.
DR GenomeRNAi; 223117; -.
DR Pharos; O95025; Tbio.
DR PRO; PR:O95025; -.
DR Proteomes; UP000005640; Chromosome 7.
DR RNAct; O95025; protein.
DR Bgee; ENSG00000153993; Expressed in buccal mucosa cell and 118 other tissues.
DR ExpressionAtlas; O95025; baseline and differential.
DR Genevisible; O95025; HS.
DR GO; GO:0005615; C:extracellular space; IBA:GO_Central.
DR GO; GO:0005887; C:integral component of plasma membrane; IBA:GO_Central.
DR GO; GO:0045499; F:chemorepellent activity; IBA:GO_Central.
DR GO; GO:0030215; F:semaphorin receptor binding; IBA:GO_Central.
DR GO; GO:0007411; P:axon guidance; IBA:GO_Central.
DR GO; GO:0050919; P:negative chemotaxis; IBA:GO_Central.
DR GO; GO:0048843; P:negative regulation of axon extension involved in axon guidance; IBA:GO_Central.
DR GO; GO:0001755; P:neural crest cell migration; IBA:GO_Central.
DR GO; GO:0030335; P:positive regulation of cell migration; IBA:GO_Central.
DR GO; GO:0071526; P:semaphorin-plexin signaling pathway; IBA:GO_Central.
DR CDD; cd11252; Sema_3D; 1.
DR Gene3D; 2.130.10.10; -; 1.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR007110; Ig-like_dom.
DR InterPro; IPR036179; Ig-like_dom_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR003599; Ig_sub.
DR InterPro; IPR041416; IL-1RAcP-like_ig.
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; PTHR11036; 1.
DR Pfam; PF18452; Ig_6; 1.
DR Pfam; PF01403; Sema; 1.
DR SMART; SM00409; IG; 1.
DR SMART; SM00423; PSI; 1.
DR SMART; SM00630; Sema; 1.
DR SUPFAM; SSF101912; SSF101912; 1.
DR SUPFAM; SSF48726; SSF48726; 1.
DR PROSITE; PS50835; IG_LIKE; 1.
DR PROSITE; PS51004; SEMA; 1.
PE 2: Evidence at transcript level;
KW Developmental protein; Differentiation; Disulfide bond; Glycoprotein;
KW Immunoglobulin domain; Neurogenesis; Reference proteome; Secreted; Signal.
FT SIGNAL 1..36
FT /evidence="ECO:0000255"
FT CHAIN 37..777
FT /note="Semaphorin-3D"
FT /id="PRO_0000032314"
FT DOMAIN 44..531
FT /note="Sema"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DOMAIN 533..585
FT /note="PSI"
FT DOMAIN 592..680
FT /note="Ig-like C2-type"
FT REGION 738..777
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 740..764
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 139
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 607
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 724
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 117..128
FT /evidence="ECO:0000250"
FT DISULFID 146..155
FT /evidence="ECO:0000250"
FT DISULFID 286..398
FT /evidence="ECO:0000250"
FT DISULFID 310..358
FT /evidence="ECO:0000250"
FT DISULFID 534..552
FT /evidence="ECO:0000250"
FT DISULFID 665..731
FT /evidence="ECO:0000250"
FT VARIANT 701
FT /note="K -> Q (in dbSNP:rs7800072)"
FT /evidence="ECO:0000269|PubMed:12975309"
FT /id="VAR_021513"
SQ SEQUENCE 777 AA; 89651 MW; 3F7B0D7AF50F53BD CRC64;
MNANKDERLK ARSQDFHLFP ALMMLSMTML FLPVTGTLKQ NIPRLKLTYK DLLLSNSCIP
FLGSSEGLDF QTLLLDEERG RLLLGAKDHI FLLSLVDLNK NFKKIYWPAA KERVELCKLA
GKDANTECAN FIRVLQPYNK THIYVCGTGA FHPICGYIDL GVYKEDIIFK LDTHNLESGR
LKCPFDPQQP FASVMTDEYL YSGTASDFLG KDTAFTRSLG PTHDHHYIRT DISEHYWLNG
AKFIGTFFIP DTYNPDDDKI YFFFRESSQE GSTSDKTILS RVGRVCKNDV GGQRSLINKW
TTFLKARLIC SIPGSDGADT YFDELQDIYL LPTRDERNPV VYGVFTTTSS IFKGSAVCVY
SMADIRAVFN GPYAHKESAD HRWVQYDGRI PYPRPGTCPS KTYDPLIKST RDFPDDVISF
IKRHSVMYKS VYPVAGGPTF KRINVDYRLT QIVVDHVIAE DGQYDVMFLG TDIGTVLKVV
SISKEKWNME EVVLEELQIF KHSSIILNME LSLKQQQLYI GSRDGLVQLS LHRCDTYGKA
CADCCLARDP YCAWDGNACS RYAPTSKRRA RRQDVKYGDP ITQCWDIEDS ISHETADEKV
IFGIEFNSTF LECIPKSQQA TIKWYIQRSG DEHREELKPD ERIIKTEYGL LIRSLQKKDS
GMYYCKAQEH TFIHTIVKLT LNVIENEQME NTQRAEHEEG KVKDLLAESR LRYKDYIQIL
SSPNFSLDQY CEQMWHREKR RQRNKGGPKW KHMQEMKKKR NRRHHRDLDE LPRAVAT
