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Q9H3T2

- SEM6C_HUMAN

UniProt

Q9H3T2 - SEM6C_HUMAN

Protein

Semaphorin-6C

Gene

SEMA6C

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 4 (30 Nov 2010)
      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: Ensembl

    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:KIAA1869, SEMAY
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:10740. 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

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35662.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2424Sequence AnalysisAdd
    BLAST
    Chaini25 – 930906Semaphorin-6CPRO_0000032344Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi70 – 701N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi111 ↔ 121PROSITE-ProRule annotation
    Disulfide bondi139 ↔ 148PROSITE-ProRule annotation
    Disulfide bondi262 ↔ 373PROSITE-ProRule annotation
    Glycosylationi286 – 2861N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi287 ↔ 332PROSITE-ProRule annotation
    Glycosylationi437 – 4371N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi479 ↔ 510PROSITE-ProRule annotation
    Disulfide bondi519 ↔ 537PROSITE-ProRule annotation
    Disulfide bondi525 ↔ 570PROSITE-ProRule annotation
    Disulfide bondi529 ↔ 545PROSITE-ProRule annotation

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    PaxDbiQ9H3T2.
    PRIDEiQ9H3T2.

    PTM databases

    PhosphoSiteiQ9H3T2.

    Expressioni

    Tissue specificityi

    In adult tissues, expressed only in skeletal muscle.1 Publication

    Gene expression databases

    ArrayExpressiQ9H3T2.
    BgeeiQ9H3T2.
    CleanExiHS_SEMA6C.
    GenevestigatoriQ9H3T2.

    Interactioni

    Protein-protein interaction databases

    STRINGi9606.ENSP00000344148.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9H3T2.
    SMRiQ9H3T2. Positions 26-544.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini25 – 604580ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini626 – 930305CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei605 – 62521HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini30 – 516487SemaPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi662 – 6676Poly-Pro
    Compositional biasi752 – 7554Poly-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.
    HOVERGENiHBG072910.
    KOiK06842.
    OMAiLVSCACR.
    OrthoDBiEOG7SV0TJ.
    PhylomeDBiQ9H3T2.
    TreeFamiTF316102.

    Family and domain databases

    Gene3Di2.130.10.10. 1 hit.
    InterProiIPR016201. Plexin-like_fold.
    IPR002165. Plexin_repeat.
    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.
    PfamiPF01437. PSI. 1 hit.
    PF01403. 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 (3)i

    Sequence statusi: Complete.

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

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9H3T2-1) [UniParc]FASTAAdd to Basket

    Also known as: Short 1

    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.

    « Hide

    MPRAPHFMPL LLLLLLLSLP HTQAAFPQDP LPLLISDLQG TSPLSWFRGL    50
    EDDAVAAELG LDFQRFLTLN RTLLVAARDH VFSFDLQAEE EGEGLVPNKY 100
    LTWRSQDVEN CAVRGKLTDE CYNYIRVLVP WDSQTLLACG TNSFSPVCRS 150
    YGITSLQQEG EELSGQARCP FDATQSNVAI FAEGSLYSAT AADFQASDAV 200
    VYRSLGPQPP LRSAKYDSKW LREPHFVQAL EHGDHVYFFF REVSVEDARL 250
    GRVQFSRVAR VCKRDMGGSP RALDRHWTSF LKLRLNCSVP GDSTFYFDVL 300
    QALTGPVNLH GRSALFGVFT TQTNSIPGSA VCAFYLDEIE RGFEGKFKEQ 350
    RSLDGAWTPV SEDRVPSPRP GSCAGVGGAA LFSSSRDLPD DVLTFIKAHP 400
    LLDPAVPPVT HQPLLTLTSR ALLTQVAVDG MAGPHSNITV MFLGSNDGTV 450
    LKVLTPGGRS GGPEPILLEE IDAYSPARCS GKRTAQTARR IIGLELDTEG 500
    HRLFVAFSGC IVYLPLSRCA RHGACQRSCL ASQDPYCGWH SSRGCVDIRG 550
    SGGTDVDQAG NQESMEHGDC QDGATGSQSG PGDSAYGVRR DLPPASASRS 600
    VPIPLLLASV AAAFALGASV SGLLVSCACR RAHRRRGKDI ETPGLPRPLS 650
    LRSLARLHGG GPEPPPPSKD GDAVQTPQLY TTFLPPPEGV PPPELACLPT 700
    PESTPELPVK HLRAAGDPWE WNQNRNNAKE GPGRSRGGHA AGGPAPRVLV 750
    RPPPPGCPGQ AVEVTTLEEL LRYLHGPQPP RKGAEPPAPL TSRALPPEPA 800
    PALLGGPSPR PHECASPLRL DVPPEGRCAS APARPALSAP APRLGVGGGR 850
    RLPFSGHRAP PALLTRVPSG GPSRYSGGPG KHLLYLGRPE GYRGRALKRV 900
    DVEKPQLSLK PPLVGPSSRQ AVPNGGRFNF 930
    Length:930
    Mass (Da):99,686
    Last modified:November 30, 2010 - v4
    Checksum:i05C2D84413208640
    GO
    Isoform 2 (identifier: Q9H3T2-2) [UniParc]FASTAAdd to Basket

    Also known as: Short 2

    The sequence of this isoform differs from the canonical sequence as follows:
         184-223: Missing.
         586-586: Y → YVLPGPGPSPGTPSPPSDAHPRPQSSTLGVHTR

    Show »
    Length:922
    Mass (Da):98,468
    Checksum:i8C201728A8F12530
    GO
    Isoform 3 (identifier: Q9H3T2-3) [UniParc]FASTAAdd to Basket

    Also known as: Long

    The sequence of this isoform differs from the canonical sequence as follows:
         586-586: Y → YVLPGPGPSPGTPSPPSDAHPRPQSSTLGVHTR

    Show »
    Length:962
    Mass (Da):102,853
    Checksum:i2A6B60559BB873E4
    GO

    Sequence cautioni

    The sequence BAB47498.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti125 – 1251I → V in AAL72099. (PubMed:12110693)Curated
    Sequence conflicti252 – 2521R → K in BAB20670. 1 PublicationCurated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti455 – 4551T → P.2 Publications
    Corresponds to variant rs4971007 [ dbSNP | Ensembl ].
    VAR_028144

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei184 – 22340Missing in isoform 2. 1 PublicationVSP_006046Add
    BLAST
    Alternative sequencei586 – 5861Y → YVLPGPGPSPGTPSPPSDAH PRPQSSTLGVHTR in isoform 2 and isoform 3. 1 PublicationVSP_006047

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF339152 mRNA. Translation: AAL72098.1.
    AF339153 mRNA. Translation: AAL72099.1.
    AF339154 mRNA. Translation: AAL72100.1.
    AB022434 mRNA. Translation: BAB20670.1.
    AB058772 mRNA. Translation: BAB47498.1. Different initiation.
    AL592424 Genomic DNA. Translation: CAI16376.1.
    AL592424 Genomic DNA. Translation: CAI16377.1.
    AL592424 Genomic DNA. Translation: CAI16378.1.
    CH471121 Genomic DNA. Translation: EAW53470.1.
    CH471121 Genomic DNA. Translation: EAW53472.1.
    CCDSiCCDS53363.1. [Q9H3T2-2]
    CCDS53364.1. [Q9H3T2-3]
    CCDS984.1. [Q9H3T2-1]
    RefSeqiNP_001171532.1. NM_001178061.1. [Q9H3T2-3]
    NP_001171533.1. NM_001178062.1. [Q9H3T2-2]
    NP_112175.2. NM_030913.4. [Q9H3T2-1]
    XP_005244890.1. XM_005244833.1. [Q9H3T2-3]
    XP_005244892.1. XM_005244835.1. [Q9H3T2-3]
    XP_005244893.1. XM_005244836.1. [Q9H3T2-1]
    UniGeneiHs.516316.

    Genome annotation databases

    EnsembliENST00000341697; ENSP00000344148; ENSG00000143434. [Q9H3T2-1]
    ENST00000368912; ENSP00000357908; ENSG00000143434. [Q9H3T2-2]
    ENST00000368913; ENSP00000357909; ENSG00000143434. [Q9H3T2-3]
    ENST00000368914; ENSP00000357910; ENSG00000143434. [Q9H3T2-1]
    GeneIDi10500.
    KEGGihsa:10500.
    UCSCiuc001ewu.3. human. [Q9H3T2-1]
    uc001ewv.3. human. [Q9H3T2-3]
    uc001eww.3. human. [Q9H3T2-2]

    Polymorphism databases

    DMDMi313104318.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF339152 mRNA. Translation: AAL72098.1 .
    AF339153 mRNA. Translation: AAL72099.1 .
    AF339154 mRNA. Translation: AAL72100.1 .
    AB022434 mRNA. Translation: BAB20670.1 .
    AB058772 mRNA. Translation: BAB47498.1 . Different initiation.
    AL592424 Genomic DNA. Translation: CAI16376.1 .
    AL592424 Genomic DNA. Translation: CAI16377.1 .
    AL592424 Genomic DNA. Translation: CAI16378.1 .
    CH471121 Genomic DNA. Translation: EAW53470.1 .
    CH471121 Genomic DNA. Translation: EAW53472.1 .
    CCDSi CCDS53363.1. [Q9H3T2-2 ]
    CCDS53364.1. [Q9H3T2-3 ]
    CCDS984.1. [Q9H3T2-1 ]
    RefSeqi NP_001171532.1. NM_001178061.1. [Q9H3T2-3 ]
    NP_001171533.1. NM_001178062.1. [Q9H3T2-2 ]
    NP_112175.2. NM_030913.4. [Q9H3T2-1 ]
    XP_005244890.1. XM_005244833.1. [Q9H3T2-3 ]
    XP_005244892.1. XM_005244835.1. [Q9H3T2-3 ]
    XP_005244893.1. XM_005244836.1. [Q9H3T2-1 ]
    UniGenei Hs.516316.

    3D structure databases

    ProteinModelPortali Q9H3T2.
    SMRi Q9H3T2. Positions 26-544.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 9606.ENSP00000344148.

    PTM databases

    PhosphoSitei Q9H3T2.

    Polymorphism databases

    DMDMi 313104318.

    Proteomic databases

    PaxDbi Q9H3T2.
    PRIDEi Q9H3T2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000341697 ; ENSP00000344148 ; ENSG00000143434 . [Q9H3T2-1 ]
    ENST00000368912 ; ENSP00000357908 ; ENSG00000143434 . [Q9H3T2-2 ]
    ENST00000368913 ; ENSP00000357909 ; ENSG00000143434 . [Q9H3T2-3 ]
    ENST00000368914 ; ENSP00000357910 ; ENSG00000143434 . [Q9H3T2-1 ]
    GeneIDi 10500.
    KEGGi hsa:10500.
    UCSCi uc001ewu.3. human. [Q9H3T2-1 ]
    uc001ewv.3. human. [Q9H3T2-3 ]
    uc001eww.3. human. [Q9H3T2-2 ]

    Organism-specific databases

    CTDi 10500.
    GeneCardsi GC01M151104.
    HGNCi HGNC:10740. SEMA6C.
    MIMi 609294. gene.
    neXtProti NX_Q9H3T2.
    PharmGKBi PA35662.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG293968.
    HOVERGENi HBG072910.
    KOi K06842.
    OMAi LVSCACR.
    OrthoDBi EOG7SV0TJ.
    PhylomeDBi Q9H3T2.
    TreeFami TF316102.

    Miscellaneous databases

    GeneWikii SEMA6C.
    GenomeRNAii 10500.
    NextBioi 39844.
    PROi Q9H3T2.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9H3T2.
    Bgeei Q9H3T2.
    CleanExi HS_SEMA6C.
    Genevestigatori Q9H3T2.

    Family and domain databases

    Gene3Di 2.130.10.10. 1 hit.
    InterProi IPR016201. Plexin-like_fold.
    IPR002165. Plexin_repeat.
    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 PF01437. PSI. 1 hit.
    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. "Identification, characterization, and functional study of the two novel human members of the semaphorin gene family."
      Qu X., Wei H., Zhai Y., Que H., Chen Q., Tang F., Wu Y., Xing G., Zhu Y., Liu S., Fan M., He F.
      J. Biol. Chem. 277:35574-35585(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), FUNCTION, TISSUE SPECIFICITY, VARIANT PRO-455.
      Tissue: Brain.
    2. Kimura T., Ishida H.
      Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Brain.
    3. "Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
      Nagase T., Nakayama M., Nakajima D., Kikuno R., Ohara O.
      DNA Res. 8:85-95(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Brain.
    4. "The DNA sequence and biological annotation of human chromosome 1."
      Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
      , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
      Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT PRO-455.

    Entry informationi

    Entry nameiSEM6C_HUMAN
    AccessioniPrimary (citable) accession number: Q9H3T2
    Secondary accession number(s): D3DV15
    , Q5JR71, Q5JR72, Q5JR73, Q8WXT8, Q8WXT9, Q8WXU0, Q96JF8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: November 30, 2010
    Last modified: October 1, 2014
    This is version 122 of the entry and version 4 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 1
      Human chromosome 1: 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