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O95025 (SEM3D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 122. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Semaphorin-3D
Gene names
Name:SEMA3D
ORF Names:UNQ760/PRO1491
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length777 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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

Subcellular location

Secreted By similarity.

Domain

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

Sequence similarities

Belongs to the semaphorin family.

Contains 1 Ig-like C2-type (immunoglobulin-like) domain.

Contains 1 PSI domain.

Contains 1 Sema domain.

Sequence caution

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

Ontologies

Keywords
   Biological processDifferentiation
Neurogenesis
   Cellular componentSecreted
   Coding sequence diversityPolymorphism
   DomainImmunoglobulin domain
Signal
   Molecular functionDevelopmental protein
   PTMDisulfide bond
Glycoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcell differentiation

Inferred from electronic annotation. Source: UniProtKB-KW

nervous system development

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentextracellular region

Inferred from electronic annotation. Source: UniProtKB-SubCell

membrane

Inferred from electronic annotation. Source: InterPro

   Molecular_functionreceptor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3636 Potential
Chain37 – 777741Semaphorin-3D
PRO_0000032314

Regions

Domain44 – 531488Sema
Domain533 – 58553PSI
Domain592 – 68089Ig-like C2-type
Compositional bias739 – 77335Arg/Lys-rich (basic)

Amino acid modifications

Glycosylation1391N-linked (GlcNAc...) Potential
Glycosylation6071N-linked (GlcNAc...) Potential
Glycosylation7241N-linked (GlcNAc...) Potential
Disulfide bond117 ↔ 128 By similarity
Disulfide bond146 ↔ 155 By similarity
Disulfide bond286 ↔ 398 By similarity
Disulfide bond310 ↔ 358 By similarity
Disulfide bond534 ↔ 552 By similarity
Disulfide bond665 ↔ 731 By similarity

Natural variations

Natural variant7011K → Q. Ref.1
Corresponds to variant rs7800072 [ dbSNP | Ensembl ].
VAR_021513

Sequences

Sequence LengthMass (Da)Tools
O95025 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: 3F7B0D7AF50F53BD

FASTA77789,651
        10         20         30         40         50         60 
MNANKDERLK ARSQDFHLFP ALMMLSMTML FLPVTGTLKQ NIPRLKLTYK DLLLSNSCIP 

        70         80         90        100        110        120 
FLGSSEGLDF QTLLLDEERG RLLLGAKDHI FLLSLVDLNK NFKKIYWPAA KERVELCKLA 

       130        140        150        160        170        180 
GKDANTECAN FIRVLQPYNK THIYVCGTGA FHPICGYIDL GVYKEDIIFK LDTHNLESGR 

       190        200        210        220        230        240 
LKCPFDPQQP FASVMTDEYL YSGTASDFLG KDTAFTRSLG PTHDHHYIRT DISEHYWLNG 

       250        260        270        280        290        300 
AKFIGTFFIP DTYNPDDDKI YFFFRESSQE GSTSDKTILS RVGRVCKNDV GGQRSLINKW 

       310        320        330        340        350        360 
TTFLKARLIC SIPGSDGADT YFDELQDIYL LPTRDERNPV VYGVFTTTSS IFKGSAVCVY 

       370        380        390        400        410        420 
SMADIRAVFN GPYAHKESAD HRWVQYDGRI PYPRPGTCPS KTYDPLIKST RDFPDDVISF 

       430        440        450        460        470        480 
IKRHSVMYKS VYPVAGGPTF KRINVDYRLT QIVVDHVIAE DGQYDVMFLG TDIGTVLKVV 

       490        500        510        520        530        540 
SISKEKWNME EVVLEELQIF KHSSIILNME LSLKQQQLYI GSRDGLVQLS LHRCDTYGKA 

       550        560        570        580        590        600 
CADCCLARDP YCAWDGNACS RYAPTSKRRA RRQDVKYGDP ITQCWDIEDS ISHETADEKV 

       610        620        630        640        650        660 
IFGIEFNSTF LECIPKSQQA TIKWYIQRSG DEHREELKPD ERIIKTEYGL LIRSLQKKDS 

       670        680        690        700        710        720 
GMYYCKAQEH TFIHTIVKLT LNVIENEQME NTQRAEHEEG KVKDLLAESR LRYKDYIQIL 

       730        740        750        760        770 
SSPNFSLDQY CEQMWHREKR RQRNKGGPKW KHMQEMKKKR NRRHHRDLDE LPRAVAT 

« Hide

References

[1]"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment."
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. expand/collapse author list , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.
Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY358937 mRNA. Translation: AAQ89296.1.
AC004957 Genomic DNA. No translation available.
BC029590 mRNA. Translation: AAH29590.1. Different initiation.
RefSeqNP_689967.2. NM_152754.2.
UniGeneHs.201340.

3D structure databases

ProteinModelPortalO95025.
SMRO95025. Positions 39-683.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000284136.

PTM databases

PhosphoSiteO95025.

Proteomic databases

PaxDbO95025.
PRIDEO95025.

Protocols and materials databases

DNASU223117.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000284136; ENSP00000284136; ENSG00000153993.
GeneID223117.
KEGGhsa:223117.
UCSCuc003uib.3. human.

Organism-specific databases

CTD223117.
GeneCardsGC07M084624.
H-InvDBHIX0006812.
HGNCHGNC:10726. SEMA3D.
HPAHPA037522.
MIM609907. gene.
neXtProtNX_O95025.
PharmGKBPA35648.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG247995.
HOGENOMHOG000039964.
HOVERGENHBG055071.
InParanoidO95025.
KOK06840.
OMAKACADCC.
OrthoDBEOG76QFGN.
PhylomeDBO95025.
TreeFamTF316102.

Gene expression databases

ArrayExpressO95025.
BgeeO95025.
CleanExHS_SEMA3D.
GenevestigatorO95025.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProIPR007110. 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]
PANTHERPTHR11036. PTHR11036. 1 hit.
PfamPF01403. Sema. 1 hit.
PF07686. V-set. 1 hit.
[Graphical view]
SMARTSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSEMA3D. human.
GenomeRNAi223117.
NextBio91714.
PROO95025.
SOURCESearch...

Entry information

Entry nameSEM3D_HUMAN
AccessionPrimary (citable) accession number: O95025
Secondary accession number(s): A6NK46, Q6UW77, Q8NCQ1
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: April 16, 2014
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM