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D3ZTD8 (SEM5A_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 33. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | 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-5A
Alternative name(s):
Semaphorin-F
Short name=Sema F
Gene names
Name:Sema5a
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length1074 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Bifunctional axonal guidance cue regulated by sulfated proteoglycans; attractive effects result from interactions with heparan sulfate proteoglycans (HSPGs), while the inhibitory effects depend on interactions with chondroitin sulfate proteoglycans (CSPGs). Ligand for receptor PLXNB3. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. May promote angiogenesis by increasing endothelial cell proliferation and migration and inhibiting apoptosis. Ref.3 Ref.4 UniProtKB Q13591 PubMed 19059233

Subunit structure

Binds PLXNB3 By similarity. UniProtKB Q13591

Subcellular location

Membrane; Single-pass membrane protein Potential.

Developmental stage

At E15.5, detected in axons extending from habenula nucleus explants (at protein level). Expressed in the habenula nucleus at E13.5 and E15.5, and in the prosomere 2 adjacent to the fasciculus retroflexus at E15.5. Ref.3 PubMed 19059233

Sequence similarities

Contains 1 PSI domain.

Contains 1 Sema domain.

Contains 6 TSP type-1 domains.

Ontologies

Keywords
   Biological processDifferentiation
Neurogenesis
   Cellular componentMembrane
   DomainRepeat
Signal
Transmembrane
Transmembrane helix
   Molecular functionDevelopmental protein
   PTMDisulfide bond
Glycoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processblood vessel endothelial cell proliferation involved in sprouting angiogenesis

Inferred from sequence or structural similarity. Source: UniProtKB

cell chemotaxis

Inferred from sequence or structural similarity. Source: UniProtKB

diencephalon development

Inferred from mutant phenotype Ref.3. Source: UniProtKB

negative regulation of GTPase activity

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of axon extension involved in axon guidance

Inferred from mutant phenotype Ref.3. Source: UniProtKB

negative regulation of endothelial cell apoptotic process

Inferred from sequence or structural similarity. Source: UniProtKB

patterning of blood vessels

Inferred from electronic annotation. Source: Ensembl

positive regulation of actin filament depolymerization

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of angiogenesis

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of axon extension involved in axon guidance

Inferred from direct assay Ref.3. Source: UniProtKB

positive regulation of catenin import into nucleus

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of endothelial cell chemotaxis

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of endothelial cell proliferation

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of protein kinase B signaling

Inferred from sequence or structural similarity. Source: UniProtKB

semaphorin-plexin signaling pathway

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentintegral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

membrane

Inferred from direct assay Ref.3. Source: UniProtKB

   Molecular_functionaxon guidance receptor activity

Inferred from electronic annotation. Source: Ensembl

chondroitin sulfate proteoglycan binding

Inferred from mutant phenotype Ref.3. Source: UniProtKB

heparan sulfate proteoglycan binding

Inferred from mutant phenotype Ref.3. Source: UniProtKB

semaphorin receptor binding

Inferred from sequence or structural similarity. Source: UniProtKB

syndecan binding

Inferred from physical interaction Ref.3. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2222 Potential
Chain23 – 10741052Semaphorin-5A
PRO_0000420236

Regions

Transmembrane969 – 98921Helical; Potential
Domain35 – 484450Sema
Domain486 – 53348PSI
Domain540 – 59354TSP type-1 1
Domain595 – 65157TSP type-1 2
Domain653 – 70250TSP type-1 3
Domain784 – 83956TSP type-1 4
Domain841 – 89656TSP type-1 5
Domain897 – 94448TSP type-1 6

Amino acid modifications

Glycosylation1471N-linked (GlcNAc...) Potential
Glycosylation1681N-linked (GlcNAc...) Potential
Glycosylation2271N-linked (GlcNAc...) Potential
Glycosylation2771N-linked (GlcNAc...) Potential
Glycosylation3231N-linked (GlcNAc...) Potential
Glycosylation3671N-linked (GlcNAc...) Potential
Glycosylation5361N-linked (GlcNAc...) Potential
Glycosylation5911N-linked (GlcNAc...) Potential
Glycosylation7171N-linked (GlcNAc...) Potential
Glycosylation8981N-linked (GlcNAc...) Potential
Glycosylation9331N-linked (GlcNAc...) Potential
Glycosylation10151N-linked (GlcNAc...) Potential
Disulfide bond104 ↔ 114 By similarity
Disulfide bond131 ↔ 140 By similarity
Disulfide bond254 ↔ 357 By similarity
Disulfide bond278 ↔ 320 By similarity
Disulfide bond607 ↔ 644 By similarity
Disulfide bond611 ↔ 650 By similarity
Disulfide bond622 ↔ 634 By similarity
Disulfide bond665 ↔ 696 By similarity
Disulfide bond669 ↔ 701 By similarity
Disulfide bond680 ↔ 686 By similarity
Disulfide bond796 ↔ 833 By similarity
Disulfide bond800 ↔ 838 By similarity
Disulfide bond811 ↔ 823 By similarity
Disulfide bond853 ↔ 890 By similarity
Disulfide bond857 ↔ 895 By similarity
Disulfide bond868 ↔ 880 By similarity

Sequences

Sequence LengthMass (Da)Tools
D3ZTD8 [UniParc].

Last modified April 20, 2010. Version 1.
Checksum: BFFBCEB5F9084FF7

FASTA1,074120,378
        10         20         30         40         50         60 
MKGACILAWL FSSLGVWRLA RPETQDPAKC QRAEHPVVSY KEIGPWLREF RAENAVDFSR 

        70         80         90        100        110        120 
LTFDPGQKEL VVGARNYLFR LQLEDLSLIQ AVQWECDEAT KKACYSKGKS KEECQNYIRV 

       130        140        150        160        170        180 
LLVGGDRLFT CGTNAFTPVC TIRSLSNLTE IHDQISGMAR CPYSPQHNST ALLTASGELY 

       190        200        210        220        230        240 
AATAMDFPGR DPAIYRSLGT LPPLRTAQYN SKWLNEPNFV SSYDIGNFTY FFFRENAVEH 

       250        260        270        280        290        300 
DCGKTVFSRA ARVCKNDIGG RFLLEDTWTT FMKARLNCSR PGEVPFYYNE LQSTFFLPEL 

       310        320        330        340        350        360 
DLIYGIFTTN VNSIAASAVC VFNLSAISQA FNGPFKYQEN SRSAWLPYPN PNPNFQCGTM 

       370        380        390        400        410        420 
DQGLYVNLTE RNLQDAQKFI LMHEVVQPVT TVPSFMEDNS RFSHVAVDVV QGRDTLVHII 

       430        440        450        460        470        480 
YLATDYGTIK KVRAPLSQSS GSCLLEEIEL FPERKSEPIR SLKILHSQSV LFVGLQEHVV 

       490        500        510        520        530        540 
KIPLKRCHFH QTRGACIGAQ DPYCGWDAVM KKCTSLEESL SMTQWDQSVP TCPTRNLTVD 

       550        560        570        580        590        600 
GSFGPWSPWT PCTHTDGTAV GSCLCRSRSC DSPAPQCGGW QCEGPRMEIT NCSRNGGWTP 

       610        620        630        640        650        660 
WTSWSPCSTT CGIGFQVRQR SCSNPTPRHG GRVCVGQNRE ERYCNEHLLC PPHVFWTGWG 

       670        680        690        700        710        720 
PWERCTAQCG GGIQARRRTC ENGPDCAGCN VEYQPCNTNA CPELKKTTPW TPWTPVNISD 

       730        740        750        760        770        780 
NGGHYEQRFR YTCKARLPDP NLLEVGRQRI EMRYCSSDGT SGCSTDGLSG DFLRAGRYSA 

       790        800        810        820        830        840 
HTVNGAWSAW TSWSQCSRDC SRGIRNRKRV CNNPEPKYGG MPCLGPSLEF QECNILPCPV 

       850        860        870        880        890        900 
DGVWSCWSSW SKCSATCGGG HYMRTRSCTN PAPAYGGDIC LGLHTEEALC NTQTCPENWS 

       910        920        930        940        950        960 
EWSEWSVCDA SGTQVRTRQC ILLFPVGSQC SGNTTESRPC VFDSNFIPEV SVARSSSVEE 

       970        980        990       1000       1010       1020 
KRCGEFNMFH MMAVGLSSSI LGCLLTLLVY TYCQRYQQQS HDATVIHPVS PAALNSSITN 

      1030       1040       1050       1060       1070 
HINKLDKYDS VEAIKAFNKN NLILEERNKY FNPHLTGKTY SNAYFTDLNN YDEY 

« Hide

References

« Hide 'large scale' references
[1]"Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M. expand/collapse author list , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Brown Norway.
[2]Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Brown Norway and Sprague-Dawley.
[3]"Semaphorin 5A is a bifunctional axon guidance cue regulated by heparan and chondroitin sulfate proteoglycans."
Kantor D.B., Chivatakarn O., Peer K.L., Oster S.F., Inatani M., Hansen M.J., Flanagan J.G., Yamaguchi Y., Sretavan D.W., Giger R.J., Kolodkin A.L.
Neuron 44:961-975(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DEVELOPMENTAL STAGE.
[4]"Semaphorin 5A and plexin-B3 inhibit human glioma cell motility through RhoGDIalpha-mediated inactivation of Rac1 GTPase."
Li X., Lee A.Y.
J. Biol. Chem. 285:32436-32445(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CH473992 Genomic DNA. Translation: EDL82657.1.
RefSeqNP_001101129.1. NM_001107659.2.
UniGeneRn.14619.

3D structure databases

ProteinModelPortalD3ZTD8.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000016506; ENSRNOP00000016506; ENSRNOG00000011977.
GeneID310207.
KEGGrno:310207.
UCSCRGD:1308650. rat.

Organism-specific databases

CTD9037.
RGD1308650. Sema5a.

Phylogenomic databases

GeneTreeENSGT00690000101974.
KOK06841.
OMAYSNAYFT.
OrthoDBEOG7SN8C0.
PhylomeDBD3ZTD8.
TreeFamTF329951.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR000884. Thrombospondin_1_rpt.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERPTHR11036. PTHR11036. 1 hit.
PfamPF01403. Sema. 1 hit.
PF00090. TSP_1. 5 hits.
[Graphical view]
SMARTSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
SM00209. TSP1. 6 hits.
[Graphical view]
SUPFAMSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
SSF82895. SSF82895. 6 hits.
PROSITEPS51004. SEMA. 1 hit.
PS50092. TSP1. 6 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio661717.
PROD3ZTD8.

Entry information

Entry nameSEM5A_RAT
AccessionPrimary (citable) accession number: D3ZTD8
Entry history
Integrated into UniProtKB/Swiss-Prot: November 28, 2012
Last sequence update: April 20, 2010
Last modified: April 16, 2014
This is version 33 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families