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Protein

Semaphorin-3D

Gene

SEMA3D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-3D
Gene namesi
Name:SEMA3D
ORF Names:UNQ760/PRO1491
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:10726. SEMA3D.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35648.

Polymorphism and mutation databases

BioMutaiSEMA3D.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3636Sequence AnalysisAdd
BLAST
Chaini37 – 777741Semaphorin-3DPRO_0000032314Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi117 ↔ 128By similarity
Glycosylationi139 – 1391N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi146 ↔ 155By similarity
Disulfide bondi286 ↔ 398By similarity
Disulfide bondi310 ↔ 358By similarity
Disulfide bondi534 ↔ 552By similarity
Glycosylationi607 – 6071N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi665 ↔ 731By similarity
Glycosylationi724 – 7241N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiO95025.
PRIDEiO95025.

PTM databases

PhosphoSiteiO95025.

Expressioni

Gene expression databases

BgeeiO95025.
CleanExiHS_SEMA3D.
ExpressionAtlasiO95025. baseline and differential.
GenevestigatoriO95025.

Organism-specific databases

HPAiHPA037522.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000284136.

Structurei

3D structure databases

ProteinModelPortaliO95025.
SMRiO95025. Positions 39-683.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini44 – 531488SemaPROSITE-ProRule annotationAdd
BLAST
Domaini533 – 58553PSIAdd
BLAST
Domaini592 – 68089Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi739 – 77335Arg/Lys-rich (basic)Add
BLAST

Domaini

Strong binding to neuropilin is mediated by the carboxy third of the protein.

Sequence similaritiesi

Belongs to the semaphorin family.Curated
Contains 1 PSI domain.Curated
Contains 1 Sema domain.PROSITE-ProRule annotation

Keywords - Domaini

Immunoglobulin domain, Signal

Phylogenomic databases

eggNOGiNOG247995.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiO95025.
KOiK06840.
OMAiQNIPRLK.
OrthoDBiEOG76QFGN.
PhylomeDBiO95025.
TreeFamiTF316102.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01403. Sema. 1 hit.
PF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O95025-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNANKDERLK ARSQDFHLFP ALMMLSMTML FLPVTGTLKQ NIPRLKLTYK
60 70 80 90 100
DLLLSNSCIP FLGSSEGLDF QTLLLDEERG RLLLGAKDHI FLLSLVDLNK
110 120 130 140 150
NFKKIYWPAA KERVELCKLA GKDANTECAN FIRVLQPYNK THIYVCGTGA
160 170 180 190 200
FHPICGYIDL GVYKEDIIFK LDTHNLESGR LKCPFDPQQP FASVMTDEYL
210 220 230 240 250
YSGTASDFLG KDTAFTRSLG PTHDHHYIRT DISEHYWLNG AKFIGTFFIP
260 270 280 290 300
DTYNPDDDKI YFFFRESSQE GSTSDKTILS RVGRVCKNDV GGQRSLINKW
310 320 330 340 350
TTFLKARLIC SIPGSDGADT YFDELQDIYL LPTRDERNPV VYGVFTTTSS
360 370 380 390 400
IFKGSAVCVY SMADIRAVFN GPYAHKESAD HRWVQYDGRI PYPRPGTCPS
410 420 430 440 450
KTYDPLIKST RDFPDDVISF IKRHSVMYKS VYPVAGGPTF KRINVDYRLT
460 470 480 490 500
QIVVDHVIAE DGQYDVMFLG TDIGTVLKVV SISKEKWNME EVVLEELQIF
510 520 530 540 550
KHSSIILNME LSLKQQQLYI GSRDGLVQLS LHRCDTYGKA CADCCLARDP
560 570 580 590 600
YCAWDGNACS RYAPTSKRRA RRQDVKYGDP ITQCWDIEDS ISHETADEKV
610 620 630 640 650
IFGIEFNSTF LECIPKSQQA TIKWYIQRSG DEHREELKPD ERIIKTEYGL
660 670 680 690 700
LIRSLQKKDS GMYYCKAQEH TFIHTIVKLT LNVIENEQME NTQRAEHEEG
710 720 730 740 750
KVKDLLAESR LRYKDYIQIL SSPNFSLDQY CEQMWHREKR RQRNKGGPKW
760 770
KHMQEMKKKR NRRHHRDLDE LPRAVAT
Length:777
Mass (Da):89,651
Last modified:May 30, 2000 - v2
Checksum:i3F7B0D7AF50F53BD
GO

Sequence cautioni

The sequence AAH29590.1 differs from that shown. Reason: Erroneous initiation. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti701 – 7011K → Q.1 Publication
Corresponds to variant rs7800072 [ dbSNP | Ensembl ].
VAR_021513

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY358937 mRNA. Translation: AAQ89296.1.
AC004957 Genomic DNA. No translation available.
BC029590 mRNA. Translation: AAH29590.1. Different initiation.
CCDSiCCDS34676.1.
RefSeqiNP_689967.2. NM_152754.2.
UniGeneiHs.201340.

Genome annotation databases

EnsembliENST00000284136; ENSP00000284136; ENSG00000153993.
GeneIDi223117.
KEGGihsa:223117.
UCSCiuc003uib.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY358937 mRNA. Translation: AAQ89296.1.
AC004957 Genomic DNA. No translation available.
BC029590 mRNA. Translation: AAH29590.1. Different initiation.
CCDSiCCDS34676.1.
RefSeqiNP_689967.2. NM_152754.2.
UniGeneiHs.201340.

3D structure databases

ProteinModelPortaliO95025.
SMRiO95025. Positions 39-683.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000284136.

PTM databases

PhosphoSiteiO95025.

Polymorphism and mutation databases

BioMutaiSEMA3D.

Proteomic databases

PaxDbiO95025.
PRIDEiO95025.

Protocols and materials databases

DNASUi223117.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000284136; ENSP00000284136; ENSG00000153993.
GeneIDi223117.
KEGGihsa:223117.
UCSCiuc003uib.3. human.

Organism-specific databases

CTDi223117.
GeneCardsiGC07M084624.
H-InvDBHIX0006812.
HGNCiHGNC:10726. SEMA3D.
HPAiHPA037522.
MIMi609907. gene.
neXtProtiNX_O95025.
PharmGKBiPA35648.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG247995.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiO95025.
KOiK06840.
OMAiQNIPRLK.
OrthoDBiEOG76QFGN.
PhylomeDBiO95025.
TreeFamiTF316102.

Miscellaneous databases

ChiTaRSiSEMA3D. human.
GenomeRNAii223117.
NextBioi91714.
PROiO95025.
SOURCEiSearch...

Gene expression databases

BgeeiO95025.
CleanExiHS_SEMA3D.
ExpressionAtlasiO95025. baseline and differential.
GenevestigatoriO95025.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01403. Sema. 1 hit.
PF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-701.
  2. "The DNA sequence of human chromosome 7."
    Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
    , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
    Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 327-777.
    Tissue: Testis.

Entry informationi

Entry nameiSEM3D_HUMAN
AccessioniPrimary (citable) accession number: O95025
Secondary accession number(s): A6NK46, Q6UW77, Q8NCQ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: April 29, 2015
This is version 127 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.