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Q9WTL3

- SEM6C_RAT

UniProt

Q9WTL3 - SEM6C_RAT

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Protein

Semaphorin-6C

Gene

Sema6c

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli

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
Complete GO annotation...

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini24 – 635612ExtracellularSequence AnalysisAdd
BLAST
Transmembranei636 – 65621HelicalSequence AnalysisAdd
BLAST
Topological domaini657 – 960304CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB-KW
Complete GO annotation...

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...

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.
GeneTreeiENSGT00760000119134.
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.

« Hide

        10         20         30         40         50
MPRAPHSMPL LLLLLLSLPQ AQTAFPQDPI PLLTSDLQGT SPSSWFRGLE
60 70 80 90 100
DDAVAAELGL DFQRFLTLNR TLLVAARDHV FSFDLQAQEE GEGLVPNKFL
110 120 130 140 150
TWRSQDMENC AVRGKLTDEC YNYIRVLVPW DSQTLLACGT NSFSPVCRSY
160 170 180 190 200
GITSLQQEGE ELSGQARCPF DATQSTVAIS AEGSLYSATA ADFQASDAVV
210 220 230 240 250
YRSLGPQPPL RSAKYDSKWL REPHFVYALE HGDHVYFFFR EVSVEDARLG
260 270 280 290 300
RVQFSRVARV CKRDMGGSPR ALDRHWTSFL KLRLNCSVPG DSTFYFDVLQ
310 320 330 340 350
SLTGPVNLHG RSALFGVFTT QTNSIPGSAV CAFYLDDIER GFEGKFKEQR
360 370 380 390 400
SLDGAWTPVS EDKVPSPRPG SCAGVGAAAL FSSSQDLPDD VLLFIKAHPL
410 420 430 440 450
LDPAVPPATH QPLLTLTSRA LLTQVAVDGM AGPHRNTTVL FLGSNDGTVL
460 470 480 490 500
KVLPPGGQSL GPEPIILEEI DAYSHARCSG KRSPRAARRI IGLELDTEGH
510 520 530 540 550
RLFVAFPGCI VYLSLSRCAR HGACQRSCLA SLDPYCGWHR FRGCVNIRGP
560 570 580 590 600
GGTDVDLTGN QESMEHGDCQ DGATGSQSGP GDSAYVLLGP GPSPETPSSP
610 620 630 640 650
SDAHPGPQSS TLGAHTQGVR RDLSPASASR SIPIPLLLAC VAAAFALGAS
660 670 680 690 700
VSGLLVSCAC RRANRRRSKD IETPGLPRPL SLRSLARLHG GGPEPPPPPK
710 720 730 740 750
DGDAAQTPQL YTTFLPPPEG GSPPELACLP TPETTPELPV KHLRASGGPW
760 770 780 790 800
EWNQNGNNAS EGPGRPRGCS AAGGPAPRVL VRPPPPGCPG QEVEVTTLEE
810 820 830 840 850
LLRYLHGPQP PRKGSEPLAS APFTSRPPAS EPGAALFVDS SPMPRDCVPP
860 870 880 890 900
LRLDVPPDGK RAAPSGRPAL SAPAPRLGVS GSRRLPFPTH RAPPGLLTRV
910 920 930 940 950
PSGGPSRYSG GPGRHLLYLG RPDGHRGRSL KRVDVKSPLS PKPPLATPPQ
960
PAPHGSHFNF
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:
EMBLi
GenBanki
DDBJi
Links Updated
AB000817 mRNA. Translation: BAA76293.2.
AB014074 mRNA. Translation: BAA76295.1.
RefSeqiNP_059004.1. NM_017308.1. [Q9WTL3-1]
XP_006232920.1. XM_006232858.2. [Q9WTL3-1]
XP_006232923.1. XM_006232861.2. [Q9WTL3-1]
XP_008759508.1. XM_008761286.1. [Q9WTL3-1]
XP_008759509.1. XM_008761287.1. [Q9WTL3-1]
XP_008759510.1. XM_008761288.1. [Q9WTL3-1]
XP_008759511.1. XM_008761289.1. [Q9WTL3-1]
XP_008759512.1. XM_008761290.1. [Q9WTL3-1]
XP_008759513.1. XM_008761291.1. [Q9WTL3-1]
XP_008759514.1. XM_008761292.1. [Q9WTL3-1]
XP_008759515.1. XM_008761293.1. [Q9WTL3-1]
XP_008759516.1. XM_008761294.1. [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:
EMBLi
GenBanki
DDBJi
Links Updated
AB000817 mRNA. Translation: BAA76293.2 .
AB014074 mRNA. Translation: BAA76295.1 .
RefSeqi NP_059004.1. NM_017308.1. [Q9WTL3-1 ]
XP_006232920.1. XM_006232858.2. [Q9WTL3-1 ]
XP_006232923.1. XM_006232861.2. [Q9WTL3-1 ]
XP_008759508.1. XM_008761286.1. [Q9WTL3-1 ]
XP_008759509.1. XM_008761287.1. [Q9WTL3-1 ]
XP_008759510.1. XM_008761288.1. [Q9WTL3-1 ]
XP_008759511.1. XM_008761289.1. [Q9WTL3-1 ]
XP_008759512.1. XM_008761290.1. [Q9WTL3-1 ]
XP_008759513.1. XM_008761291.1. [Q9WTL3-1 ]
XP_008759514.1. XM_008761292.1. [Q9WTL3-1 ]
XP_008759515.1. XM_008761293.1. [Q9WTL3-1 ]
XP_008759516.1. XM_008761294.1. [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 ENSGT00760000119134.
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: November 26, 2014
This is version 113 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