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Q9WTL3

- SEM6C_RAT

UniProt

Q9WTL3 - SEM6C_RAT

Protein

Semaphorin-6C

Gene

Sema6c

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 1 (01 Nov 1999)
      Previous versions | rss
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    Functioni

    Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.1 Publication

    GO - Molecular functioni

    1. receptor activity Source: InterPro

    GO - Biological processi

    1. axon guidance Source: RGD

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Differentiation, Neurogenesis

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Semaphorin-6C
    Alternative name(s):
    Semaphorin-Y
    Short name:
    Sema Y
    Gene namesi
    Name:Sema6c
    Synonyms:Semay
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 2

    Organism-specific databases

    RGDi3659. Sema6c.

    Subcellular locationi

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cell membrane, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2323Sequence AnalysisAdd
    BLAST
    Chaini24 – 960937Semaphorin-6CPRO_0000032346Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi69 – 691N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi110 ↔ 120PROSITE-ProRule annotation
    Disulfide bondi138 ↔ 147PROSITE-ProRule annotation
    Disulfide bondi261 ↔ 372PROSITE-ProRule annotation
    Glycosylationi285 – 2851N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi286 ↔ 331PROSITE-ProRule annotation
    Glycosylationi436 – 4361N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi478 ↔ 509PROSITE-ProRule annotation
    Disulfide bondi518 ↔ 536PROSITE-ProRule annotation
    Disulfide bondi524 ↔ 569PROSITE-ProRule annotation
    Disulfide bondi528 ↔ 544PROSITE-ProRule annotation

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    PaxDbiQ9WTL3.
    PRIDEiQ9WTL3.

    PTM databases

    PhosphoSiteiQ9WTL3.

    Expressioni

    Tissue specificityi

    Expressed in many regions of the developing nervous system, probably in neurons and their precursors, but also in nonneural tissue such as immature muscle and dermis. In adult, strong expression in the skeletal muscle and moderate expression in the brain, where cerebellum shows the highest expression. Also expressed in almost all areas of the CNS.

    Developmental stagei

    Detected at E12 and found at markedly increased levels at E15 and E18 in both the head and the body. At birth the level decreases significantly.

    Gene expression databases

    GenevestigatoriQ9WTL3.

    Interactioni

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000050221.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9WTL3.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini24 – 635612ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini657 – 960304CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei636 – 65621HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini29 – 515487SemaPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi693 – 6997Poly-Pro
    Compositional biasi783 – 7864Poly-Pro

    Sequence similaritiesi

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

    Keywords - Domaini

    Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG293968.
    GeneTreeiENSGT00690000101956.
    HOGENOMiHOG000232047.
    HOVERGENiHBG072910.
    InParanoidiQ9WTL3.
    KOiK06842.
    OMAiLVSCACR.
    OrthoDBiEOG7SV0TJ.
    PhylomeDBiQ9WTL3.
    TreeFamiTF316102.

    Family and domain databases

    Gene3Di2.130.10.10. 1 hit.
    InterProiIPR016201. Plexin-like_fold.
    IPR001627. Semap_dom.
    IPR027231. Semaphorin.
    IPR015514. Semaphorin_6C.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view]
    PANTHERiPTHR11036. PTHR11036. 1 hit.
    PTHR11036:SF11. PTHR11036:SF11. 1 hit.
    PfamiPF01403. Sema. 1 hit.
    [Graphical view]
    SMARTiSM00423. PSI. 1 hit.
    SM00630. Sema. 1 hit.
    [Graphical view]
    SUPFAMiSSF101912. SSF101912. 1 hit.
    SSF103575. SSF103575. 1 hit.
    PROSITEiPS51004. SEMA. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

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

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform Sema Y-L (identifier: Q9WTL3-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

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    MPRAPHSMPL LLLLLLSLPQ AQTAFPQDPI PLLTSDLQGT SPSSWFRGLE    50
    DDAVAAELGL DFQRFLTLNR TLLVAARDHV FSFDLQAQEE GEGLVPNKFL 100
    TWRSQDMENC AVRGKLTDEC YNYIRVLVPW DSQTLLACGT NSFSPVCRSY 150
    GITSLQQEGE ELSGQARCPF DATQSTVAIS AEGSLYSATA ADFQASDAVV 200
    YRSLGPQPPL RSAKYDSKWL REPHFVYALE HGDHVYFFFR EVSVEDARLG 250
    RVQFSRVARV CKRDMGGSPR ALDRHWTSFL KLRLNCSVPG DSTFYFDVLQ 300
    SLTGPVNLHG RSALFGVFTT QTNSIPGSAV CAFYLDDIER GFEGKFKEQR 350
    SLDGAWTPVS EDKVPSPRPG SCAGVGAAAL FSSSQDLPDD VLLFIKAHPL 400
    LDPAVPPATH QPLLTLTSRA LLTQVAVDGM AGPHRNTTVL FLGSNDGTVL 450
    KVLPPGGQSL GPEPIILEEI DAYSHARCSG KRSPRAARRI IGLELDTEGH 500
    RLFVAFPGCI VYLSLSRCAR HGACQRSCLA SLDPYCGWHR FRGCVNIRGP 550
    GGTDVDLTGN QESMEHGDCQ DGATGSQSGP GDSAYVLLGP GPSPETPSSP 600
    SDAHPGPQSS TLGAHTQGVR RDLSPASASR SIPIPLLLAC VAAAFALGAS 650
    VSGLLVSCAC RRANRRRSKD IETPGLPRPL SLRSLARLHG GGPEPPPPPK 700
    DGDAAQTPQL YTTFLPPPEG GSPPELACLP TPETTPELPV KHLRASGGPW 750
    EWNQNGNNAS EGPGRPRGCS AAGGPAPRVL VRPPPPGCPG QEVEVTTLEE 800
    LLRYLHGPQP PRKGSEPLAS APFTSRPPAS EPGAALFVDS SPMPRDCVPP 850
    LRLDVPPDGK RAAPSGRPAL SAPAPRLGVS GSRRLPFPTH RAPPGLLTRV 900
    PSGGPSRYSG GPGRHLLYLG RPDGHRGRSL KRVDVKSPLS PKPPLATPPQ 950
    PAPHGSHFNF 960
    Length:960
    Mass (Da):102,610
    Last modified:November 1, 1999 - v1
    Checksum:iC88293C5607E6086
    GO
    Isoform Sema Y-S (identifier: Q9WTL3-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         586-617: Missing.

    Show »
    Length:928
    Mass (Da):99,521
    Checksum:i386B08143D19FCDC
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei586 – 61732Missing in isoform Sema Y-S. 1 PublicationVSP_006048Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB000817 mRNA. Translation: BAA76293.2.
    AB014074 mRNA. Translation: BAA76295.1.
    RefSeqiNP_059004.1. NM_017308.1. [Q9WTL3-1]
    XP_006232919.1. XM_006232857.1. [Q9WTL3-1]
    XP_006232920.1. XM_006232858.1. [Q9WTL3-1]
    XP_006232921.1. XM_006232859.1. [Q9WTL3-1]
    XP_006232922.1. XM_006232860.1. [Q9WTL3-1]
    XP_006232923.1. XM_006232861.1. [Q9WTL3-1]
    XP_006232924.1. XM_006232862.1. [Q9WTL3-1]
    XP_006232925.1. XM_006232863.1. [Q9WTL3-1]
    XP_006232926.1. XM_006232864.1. [Q9WTL3-1]
    XP_006232927.1. XM_006232865.1. [Q9WTL3-1]
    XP_006232928.1. XM_006232866.1. [Q9WTL3-1]
    XP_006232929.1. XM_006232867.1. [Q9WTL3-1]
    XP_006232930.1. XM_006232868.1. [Q9WTL3-2]
    UniGeneiRn.22449.

    Genome annotation databases

    EnsembliENSRNOT00000028645; ENSRNOP00000028645; ENSRNOG00000021101. [Q9WTL3-2]
    ENSRNOT00000050914; ENSRNOP00000050221; ENSRNOG00000021101. [Q9WTL3-1]
    GeneIDi29744.
    KEGGirno:29744.
    UCSCiRGD:3659. rat. [Q9WTL3-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB000817 mRNA. Translation: BAA76293.2 .
    AB014074 mRNA. Translation: BAA76295.1 .
    RefSeqi NP_059004.1. NM_017308.1. [Q9WTL3-1 ]
    XP_006232919.1. XM_006232857.1. [Q9WTL3-1 ]
    XP_006232920.1. XM_006232858.1. [Q9WTL3-1 ]
    XP_006232921.1. XM_006232859.1. [Q9WTL3-1 ]
    XP_006232922.1. XM_006232860.1. [Q9WTL3-1 ]
    XP_006232923.1. XM_006232861.1. [Q9WTL3-1 ]
    XP_006232924.1. XM_006232862.1. [Q9WTL3-1 ]
    XP_006232925.1. XM_006232863.1. [Q9WTL3-1 ]
    XP_006232926.1. XM_006232864.1. [Q9WTL3-1 ]
    XP_006232927.1. XM_006232865.1. [Q9WTL3-1 ]
    XP_006232928.1. XM_006232866.1. [Q9WTL3-1 ]
    XP_006232929.1. XM_006232867.1. [Q9WTL3-1 ]
    XP_006232930.1. XM_006232868.1. [Q9WTL3-2 ]
    UniGenei Rn.22449.

    3D structure databases

    ProteinModelPortali Q9WTL3.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10116.ENSRNOP00000050221.

    PTM databases

    PhosphoSitei Q9WTL3.

    Proteomic databases

    PaxDbi Q9WTL3.
    PRIDEi Q9WTL3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000028645 ; ENSRNOP00000028645 ; ENSRNOG00000021101 . [Q9WTL3-2 ]
    ENSRNOT00000050914 ; ENSRNOP00000050221 ; ENSRNOG00000021101 . [Q9WTL3-1 ]
    GeneIDi 29744.
    KEGGi rno:29744.
    UCSCi RGD:3659. rat. [Q9WTL3-1 ]

    Organism-specific databases

    CTDi 10500.
    RGDi 3659. Sema6c.

    Phylogenomic databases

    eggNOGi NOG293968.
    GeneTreei ENSGT00690000101956.
    HOGENOMi HOG000232047.
    HOVERGENi HBG072910.
    InParanoidi Q9WTL3.
    KOi K06842.
    OMAi LVSCACR.
    OrthoDBi EOG7SV0TJ.
    PhylomeDBi Q9WTL3.
    TreeFami TF316102.

    Miscellaneous databases

    NextBioi 610256.
    PROi Q9WTL3.

    Gene expression databases

    Genevestigatori Q9WTL3.

    Family and domain databases

    Gene3Di 2.130.10.10. 1 hit.
    InterProi IPR016201. Plexin-like_fold.
    IPR001627. Semap_dom.
    IPR027231. Semaphorin.
    IPR015514. Semaphorin_6C.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view ]
    PANTHERi PTHR11036. PTHR11036. 1 hit.
    PTHR11036:SF11. PTHR11036:SF11. 1 hit.
    Pfami PF01403. Sema. 1 hit.
    [Graphical view ]
    SMARTi SM00423. PSI. 1 hit.
    SM00630. Sema. 1 hit.
    [Graphical view ]
    SUPFAMi SSF101912. SSF101912. 1 hit.
    SSF103575. SSF103575. 1 hit.
    PROSITEi PS51004. SEMA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of a novel class VI semaphorin, semaphorin Y."
      Kikuchi K., Chedotal A., Hanafusa H., Ujimasa Y., de Castro F., Goodman C.S., Kimura T.
      Mol. Cell. Neurosci. 13:9-23(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS SEMA Y-L AND SEMA Y-S), FUNCTION.
      Strain: Sprague-Dawley.
      Tissue: Muscle.

    Entry informationi

    Entry nameiSEM6C_RAT
    AccessioniPrimary (citable) accession number: Q9WTL3
    Secondary accession number(s): Q9WTM6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1999
    Last modified: October 1, 2014
    This is version 111 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