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Q9WTL3 (SEM6C_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 110. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Semaphorin-6C
Alternative name(s):
Semaphorin-Y
Short name=Sema Y
Gene names
Name:Sema6c
Synonyms:Semay
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length960 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.1

Subcellular location

Cell membrane; Single-pass type I membrane protein.

Tissue specificity

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 stage

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.

Sequence similarities

Belongs to the semaphorin family.

Contains 1 PSI domain.

Contains 1 Sema domain.

Ontologies

Keywords
   Biological processDifferentiation
Neurogenesis
   Cellular componentCell membrane
Membrane
   Coding sequence diversityAlternative splicing
   DomainSignal
Transmembrane
Transmembrane helix
   Molecular functionDevelopmental protein
   PTMDisulfide bond
Glycoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processaxon guidance

Inferred from direct assay Ref.1. Source: RGD

   Cellular_componentintegral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionreceptor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform Sema Y-L (identifier: Q9WTL3-1)

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.
Isoform Sema Y-S (identifier: Q9WTL3-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2323 Potential
Chain24 – 960937Semaphorin-6C
PRO_0000032346

Regions

Topological domain24 – 635612Extracellular Potential
Transmembrane636 – 65621Helical; Potential
Topological domain657 – 960304Cytoplasmic Potential
Domain29 – 515487Sema
Compositional bias693 – 6997Poly-Pro
Compositional bias783 – 7864Poly-Pro

Amino acid modifications

Glycosylation691N-linked (GlcNAc...) Potential
Glycosylation2851N-linked (GlcNAc...) Potential
Glycosylation4361N-linked (GlcNAc...) Potential
Disulfide bond110 ↔ 120 By similarity
Disulfide bond138 ↔ 147 By similarity
Disulfide bond261 ↔ 372 By similarity
Disulfide bond286 ↔ 331 By similarity
Disulfide bond478 ↔ 509 By similarity
Disulfide bond518 ↔ 536 By similarity
Disulfide bond524 ↔ 569 By similarity
Disulfide bond528 ↔ 544 By similarity

Natural variations

Alternative sequence586 – 61732Missing in isoform Sema Y-S.
VSP_006048

Sequences

Sequence LengthMass (Da)Tools
Isoform Sema Y-L [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: C88293C5607E6086

FASTA960102,610
        10         20         30         40         50         60 
MPRAPHSMPL LLLLLLSLPQ AQTAFPQDPI PLLTSDLQGT SPSSWFRGLE DDAVAAELGL 

        70         80         90        100        110        120 
DFQRFLTLNR TLLVAARDHV FSFDLQAQEE GEGLVPNKFL TWRSQDMENC AVRGKLTDEC 

       130        140        150        160        170        180 
YNYIRVLVPW DSQTLLACGT NSFSPVCRSY GITSLQQEGE ELSGQARCPF DATQSTVAIS 

       190        200        210        220        230        240 
AEGSLYSATA ADFQASDAVV YRSLGPQPPL RSAKYDSKWL REPHFVYALE HGDHVYFFFR 

       250        260        270        280        290        300 
EVSVEDARLG RVQFSRVARV CKRDMGGSPR ALDRHWTSFL KLRLNCSVPG DSTFYFDVLQ 

       310        320        330        340        350        360 
SLTGPVNLHG RSALFGVFTT QTNSIPGSAV CAFYLDDIER GFEGKFKEQR SLDGAWTPVS 

       370        380        390        400        410        420 
EDKVPSPRPG SCAGVGAAAL FSSSQDLPDD VLLFIKAHPL LDPAVPPATH QPLLTLTSRA 

       430        440        450        460        470        480 
LLTQVAVDGM AGPHRNTTVL FLGSNDGTVL KVLPPGGQSL GPEPIILEEI DAYSHARCSG 

       490        500        510        520        530        540 
KRSPRAARRI IGLELDTEGH RLFVAFPGCI VYLSLSRCAR HGACQRSCLA SLDPYCGWHR 

       550        560        570        580        590        600 
FRGCVNIRGP GGTDVDLTGN QESMEHGDCQ DGATGSQSGP GDSAYVLLGP GPSPETPSSP 

       610        620        630        640        650        660 
SDAHPGPQSS TLGAHTQGVR RDLSPASASR SIPIPLLLAC VAAAFALGAS VSGLLVSCAC 

       670        680        690        700        710        720 
RRANRRRSKD IETPGLPRPL SLRSLARLHG GGPEPPPPPK DGDAAQTPQL YTTFLPPPEG 

       730        740        750        760        770        780 
GSPPELACLP TPETTPELPV KHLRASGGPW EWNQNGNNAS EGPGRPRGCS AAGGPAPRVL 

       790        800        810        820        830        840 
VRPPPPGCPG QEVEVTTLEE LLRYLHGPQP PRKGSEPLAS APFTSRPPAS EPGAALFVDS 

       850        860        870        880        890        900 
SPMPRDCVPP LRLDVPPDGK RAAPSGRPAL SAPAPRLGVS GSRRLPFPTH RAPPGLLTRV 

       910        920        930        940        950        960 
PSGGPSRYSG GPGRHLLYLG RPDGHRGRSL KRVDVKSPLS PKPPLATPPQ PAPHGSHFNF 

« Hide

Isoform Sema Y-S [UniParc].

Checksum: 386B08143D19FCDC
Show »

FASTA92899,521

References

[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB000817 mRNA. Translation: BAA76293.2.
AB014074 mRNA. Translation: BAA76295.1.
RefSeqNP_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]
UniGeneRn.22449.

3D structure databases

ProteinModelPortalQ9WTL3.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000050221.

PTM databases

PhosphoSiteQ9WTL3.

Proteomic databases

PaxDbQ9WTL3.
PRIDEQ9WTL3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000028645; ENSRNOP00000028645; ENSRNOG00000021101. [Q9WTL3-2]
ENSRNOT00000050914; ENSRNOP00000050221; ENSRNOG00000021101. [Q9WTL3-1]
GeneID29744.
KEGGrno:29744.
UCSCRGD:3659. rat. [Q9WTL3-1]

Organism-specific databases

CTD10500.
RGD3659. Sema6c.

Phylogenomic databases

eggNOGNOG293968.
GeneTreeENSGT00690000101956.
HOGENOMHOG000232047.
HOVERGENHBG072910.
InParanoidQ9WTL3.
KOK06842.
OMALVSCACR.
OrthoDBEOG7SV0TJ.
PhylomeDBQ9WTL3.
TreeFamTF316102.

Gene expression databases

GenevestigatorQ9WTL3.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015514. Semaphorin_6C.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERPTHR11036. PTHR11036. 1 hit.
PTHR11036:SF11. PTHR11036:SF11. 1 hit.
PfamPF01403. Sema. 1 hit.
[Graphical view]
SMARTSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEPS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio610256.
PROQ9WTL3.

Entry information

Entry nameSEM6C_RAT
AccessionPrimary (citable) accession number: Q9WTL3
Secondary accession number(s): Q9WTM6
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: June 11, 2014
This is version 110 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