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D3ZTD8

- SEM5A_RAT

UniProt

D3ZTD8 - SEM5A_RAT

Protein

Semaphorin-5A

Gene

Sema5a

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 35 (01 Oct 2014)
      Sequence version 1 (20 Apr 2010)
      Previous versions | rss
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    Functioni

    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.By similarity2 Publications

    GO - Molecular functioni

    1. axon guidance receptor activity Source: Ensembl
    2. chondroitin sulfate proteoglycan binding Source: UniProtKB
    3. heparan sulfate proteoglycan binding Source: UniProtKB
    4. semaphorin receptor binding Source: UniProtKB
    5. syndecan binding Source: UniProtKB

    GO - Biological processi

    1. axonal fasciculation Source: UniProtKB
    2. blood vessel endothelial cell proliferation involved in sprouting angiogenesis Source: UniProtKB
    3. cell chemotaxis Source: UniProtKB
    4. diencephalon development Source: UniProtKB
    5. negative regulation of axon extension involved in axon guidance Source: UniProtKB
    6. negative regulation of cell adhesion Source: UniProtKB
    7. negative regulation of endothelial cell apoptotic process Source: UniProtKB
    8. patterning of blood vessels Source: Ensembl
    9. positive chemotaxis Source: UniProtKB
    10. positive regulation of actin filament depolymerization Source: UniProtKB
    11. positive regulation of angiogenesis Source: UniProtKB
    12. positive regulation of axon extension involved in axon guidance Source: UniProtKB
    13. positive regulation of catenin import into nucleus Source: UniProtKB
    14. positive regulation of endothelial cell chemotaxis Source: UniProtKB
    15. positive regulation of endothelial cell proliferation Source: UniProtKB
    16. positive regulation of protein kinase B signaling Source: UniProtKB
    17. semaphorin-plexin signaling pathway Source: UniProtKB
    18. signal clustering Source: UniProtKB

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Differentiation, Neurogenesis

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Semaphorin-5ABy similarity
    Alternative name(s):
    Semaphorin-F
    Short name:
    Sema F
    Gene namesi
    Name:Sema5aImported
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 2

    Organism-specific databases

    RGDi1308650. Sema5a.

    Subcellular locationi

    Membrane Sequence Analysis; Single-pass membrane protein Sequence Analysis

    GO - Cellular componenti

    1. integral component of membrane Source: UniProtKB-KW
    2. membrane Source: UniProtKB

    Keywords - Cellular componenti

    Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2222Sequence AnalysisAdd
    BLAST
    Chaini23 – 10741052Semaphorin-5ASequence AnalysisPRO_0000420236Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi104 ↔ 114Sequence Analysis
    Disulfide bondi131 ↔ 140Sequence Analysis
    Glycosylationi147 – 1471N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi168 – 1681N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi227 – 2271N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi254 ↔ 357Sequence Analysis
    Glycosylationi277 – 2771N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi278 ↔ 320Sequence Analysis
    Glycosylationi323 – 3231N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi367 – 3671N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi536 – 5361N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi591 – 5911N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi607 ↔ 644Sequence Analysis
    Disulfide bondi611 ↔ 650Sequence Analysis
    Disulfide bondi622 ↔ 634Sequence Analysis
    Disulfide bondi665 ↔ 696Sequence Analysis
    Disulfide bondi669 ↔ 701Sequence Analysis
    Disulfide bondi680 ↔ 686Sequence Analysis
    Glycosylationi717 – 7171N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi796 ↔ 833Sequence Analysis
    Disulfide bondi800 ↔ 838Sequence Analysis
    Disulfide bondi811 ↔ 823Sequence Analysis
    Disulfide bondi853 ↔ 890Sequence Analysis
    Disulfide bondi857 ↔ 895Sequence Analysis
    Disulfide bondi868 ↔ 880Sequence Analysis
    Glycosylationi898 – 8981N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi933 – 9331N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi1015 – 10151N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Expressioni

    Developmental stagei

    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 E15.5.1 Publication

    Interactioni

    Subunit structurei

    Binds PLXNB3.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliD3ZTD8.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei969 – 98921HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini35 – 484450SemaPROSITE-ProRule annotationAdd
    BLAST
    Domaini486 – 53348PSISequence AnalysisAdd
    BLAST
    Domaini540 – 59354TSP type-1 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini595 – 65157TSP type-1 2PROSITE-ProRule annotationAdd
    BLAST
    Domaini653 – 70250TSP type-1 3PROSITE-ProRule annotationAdd
    BLAST
    Domaini784 – 83956TSP type-1 4PROSITE-ProRule annotationAdd
    BLAST
    Domaini841 – 89656TSP type-1 5PROSITE-ProRule annotationAdd
    BLAST
    Domaini897 – 94448TSP type-1 6PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 PSI domain.Sequence Analysis
    Contains 1 Sema domain.PROSITE-ProRule annotation
    Contains 6 TSP type-1 domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    GeneTreeiENSGT00690000101974.
    KOiK06841.
    OMAiYSNAYFT.
    OrthoDBiEOG7SN8C0.
    PhylomeDBiD3ZTD8.
    TreeFamiTF329951.

    Family and domain databases

    Gene3Di2.130.10.10. 1 hit.
    InterProiIPR016201. Plexin-like_fold.
    IPR001627. Semap_dom.
    IPR027231. Semaphorin.
    IPR000884. Thrombospondin_1_rpt.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view]
    PANTHERiPTHR11036. PTHR11036. 1 hit.
    PfamiPF01403. Sema. 1 hit.
    PF00090. TSP_1. 5 hits.
    [Graphical view]
    SMARTiSM00423. PSI. 1 hit.
    SM00630. Sema. 1 hit.
    SM00209. TSP1. 6 hits.
    [Graphical view]
    SUPFAMiSSF101912. SSF101912. 1 hit.
    SSF103575. SSF103575. 1 hit.
    SSF82895. SSF82895. 6 hits.
    PROSITEiPS51004. SEMA. 1 hit.
    PS50092. TSP1. 6 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    D3ZTD8-1 [UniParc]FASTAAdd to Basket

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    MKGACILAWL FSSLGVWRLA RPETQDPAKC QRAEHPVVSY KEIGPWLREF     50
    RAENAVDFSR LTFDPGQKEL VVGARNYLFR LQLEDLSLIQ AVQWECDEAT 100
    KKACYSKGKS KEECQNYIRV LLVGGDRLFT CGTNAFTPVC TIRSLSNLTE 150
    IHDQISGMAR CPYSPQHNST ALLTASGELY AATAMDFPGR DPAIYRSLGT 200
    LPPLRTAQYN SKWLNEPNFV SSYDIGNFTY FFFRENAVEH DCGKTVFSRA 250
    ARVCKNDIGG RFLLEDTWTT FMKARLNCSR PGEVPFYYNE LQSTFFLPEL 300
    DLIYGIFTTN VNSIAASAVC VFNLSAISQA FNGPFKYQEN SRSAWLPYPN 350
    PNPNFQCGTM DQGLYVNLTE RNLQDAQKFI LMHEVVQPVT TVPSFMEDNS 400
    RFSHVAVDVV QGRDTLVHII YLATDYGTIK KVRAPLSQSS GSCLLEEIEL 450
    FPERKSEPIR SLKILHSQSV LFVGLQEHVV KIPLKRCHFH QTRGACIGAQ 500
    DPYCGWDAVM KKCTSLEESL SMTQWDQSVP TCPTRNLTVD GSFGPWSPWT 550
    PCTHTDGTAV GSCLCRSRSC DSPAPQCGGW QCEGPRMEIT NCSRNGGWTP 600
    WTSWSPCSTT CGIGFQVRQR SCSNPTPRHG GRVCVGQNRE ERYCNEHLLC 650
    PPHVFWTGWG PWERCTAQCG GGIQARRRTC ENGPDCAGCN VEYQPCNTNA 700
    CPELKKTTPW TPWTPVNISD NGGHYEQRFR YTCKARLPDP NLLEVGRQRI 750
    EMRYCSSDGT SGCSTDGLSG DFLRAGRYSA HTVNGAWSAW TSWSQCSRDC 800
    SRGIRNRKRV CNNPEPKYGG MPCLGPSLEF QECNILPCPV DGVWSCWSSW 850
    SKCSATCGGG HYMRTRSCTN PAPAYGGDIC LGLHTEEALC NTQTCPENWS 900
    EWSEWSVCDA SGTQVRTRQC ILLFPVGSQC SGNTTESRPC VFDSNFIPEV 950
    SVARSSSVEE KRCGEFNMFH MMAVGLSSSI LGCLLTLLVY TYCQRYQQQS 1000
    HDATVIHPVS PAALNSSITN HINKLDKYDS VEAIKAFNKN NLILEERNKY 1050
    FNPHLTGKTY SNAYFTDLNN YDEY 1074
    Length:1,074
    Mass (Da):120,378
    Last modified:April 20, 2010 - v1
    Checksum:iBFFBCEB5F9084FF7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CH473992 Genomic DNA. Translation: EDL82657.1.
    RefSeqiNP_001101129.1. NM_001107659.2.
    UniGeneiRn.14619.

    Genome annotation databases

    EnsembliENSRNOT00000016506; ENSRNOP00000016506; ENSRNOG00000011977.
    GeneIDi310207.
    KEGGirno:310207.
    UCSCiRGD:1308650. rat.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CH473992 Genomic DNA. Translation: EDL82657.1 .
    RefSeqi NP_001101129.1. NM_001107659.2.
    UniGenei Rn.14619.

    3D structure databases

    ProteinModelPortali D3ZTD8.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000016506 ; ENSRNOP00000016506 ; ENSRNOG00000011977 .
    GeneIDi 310207.
    KEGGi rno:310207.
    UCSCi RGD:1308650. rat.

    Organism-specific databases

    CTDi 9037.
    RGDi 1308650. Sema5a.

    Phylogenomic databases

    GeneTreei ENSGT00690000101974.
    KOi K06841.
    OMAi YSNAYFT.
    OrthoDBi EOG7SN8C0.
    PhylomeDBi D3ZTD8.
    TreeFami TF329951.

    Miscellaneous databases

    NextBioi 661717.
    PROi D3ZTD8.

    Family and domain databases

    Gene3Di 2.130.10.10. 1 hit.
    InterProi IPR016201. Plexin-like_fold.
    IPR001627. Semap_dom.
    IPR027231. Semaphorin.
    IPR000884. Thrombospondin_1_rpt.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view ]
    PANTHERi PTHR11036. PTHR11036. 1 hit.
    Pfami PF01403. Sema. 1 hit.
    PF00090. TSP_1. 5 hits.
    [Graphical view ]
    SMARTi SM00423. PSI. 1 hit.
    SM00630. Sema. 1 hit.
    SM00209. TSP1. 6 hits.
    [Graphical view ]
    SUPFAMi SSF101912. SSF101912. 1 hit.
    SSF103575. SSF103575. 1 hit.
    SSF82895. SSF82895. 6 hits.
    PROSITEi PS51004. SEMA. 1 hit.
    PS50092. TSP1. 6 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.
      , 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 NorwayImported.
    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 NorwayImported and Sprague-DawleyImported.
    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.

    Entry informationi

    Entry nameiSEM5A_RAT
    AccessioniPrimary (citable) accession number: D3ZTD8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 28, 2012
    Last sequence update: April 20, 2010
    Last modified: October 1, 2014
    This is version 35 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3