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Protein

Semaphorin-6C

Gene

Sema6c

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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 - Biological processi

  • axon guidance Source: RGD

Keywordsi

Molecular functionDevelopmental protein
Biological processDifferentiation, 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 2

Organism-specific databases

RGDi3659 Sema6c

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini24 – 635ExtracellularSequence analysisAdd BLAST612
Transmembranei636 – 656HelicalSequence analysisAdd BLAST21
Topological domaini657 – 960CytoplasmicSequence analysisAdd BLAST304

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000003234624 – 960Semaphorin-6CAdd BLAST937

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi69N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi110 ↔ 120PROSITE-ProRule annotation
Disulfide bondi138 ↔ 147PROSITE-ProRule annotation
Disulfide bondi261 ↔ 372PROSITE-ProRule annotation
Glycosylationi285N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi286 ↔ 331PROSITE-ProRule annotation
Glycosylationi436N-linked (GlcNAc...) asparagineSequence analysis1
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

PTM databases

iPTMnetiQ9WTL3
PhosphoSitePlusiQ9WTL3

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

BgeeiENSRNOG00000021101
ExpressionAtlasiQ9WTL3 baseline and differential
GenevisibleiQ9WTL3 RN

Interactioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000050221

Structurei

3D structure databases

ProteinModelPortaliQ9WTL3
SMRiQ9WTL3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 515SemaPROSITE-ProRule annotationAdd BLAST487

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi693 – 699Poly-Pro7
Compositional biasi783 – 786Poly-Pro4

Sequence similaritiesi

Belongs to the semaphorin family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3611 Eukaryota
ENOG410XQZC LUCA
GeneTreeiENSGT00760000119134
HOGENOMiHOG000232047
HOVERGENiHBG072910
InParanoidiQ9WTL3
KOiK06842
OMAiLVSCACR
OrthoDBiEOG091G014B
PhylomeDBiQ9WTL3
TreeFamiTF316102

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR001627 Semap_dom
IPR036352 Semap_dom_sf
IPR027231 Semaphorin
IPR015514 Semaphorin_6C
IPR015943 WD40/YVTN_repeat-like_dom_sf
PANTHERiPTHR11036 PTHR11036, 1 hit
PTHR11036:SF11 PTHR11036:SF11, 1 hit
PfamiView protein in Pfam
PF01403 Sema, 1 hit
SMARTiView protein in SMART
SM00630 Sema, 1 hit
SUPFAMiSSF101912 SSF101912, 1 hit
PROSITEiView protein in PROSITE
PS51004 SEMA, 1 hit

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. AlignAdd to basket

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)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_006048586 – 617Missing in isoform Sema Y-S. 1 PublicationAdd BLAST32

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_006232858.3 [Q9WTL3-1]
XP_006232923.1, XM_006232861.3 [Q9WTL3-1]
XP_008759512.1, XM_008761290.2 [Q9WTL3-1]
XP_008759515.1, XM_008761293.2 [Q9WTL3-1]
XP_017446288.1, XM_017590799.1 [Q9WTL3-1]
XP_017446289.1, XM_017590800.1 [Q9WTL3-1]
XP_017446290.1, XM_017590801.1 [Q9WTL3-1]
XP_017446291.1, XM_017590802.1 [Q9WTL3-1]
XP_017446292.1, XM_017590803.1 [Q9WTL3-1]
XP_017446293.1, XM_017590804.1 [Q9WTL3-1]
XP_017446294.1, XM_017590805.1 [Q9WTL3-1]
XP_017446295.1, XM_017590806.1 [Q9WTL3-1]
XP_017446296.1, XM_017590807.1 [Q9WTL3-1]
XP_017446297.1, XM_017590808.1 [Q9WTL3-1]
XP_017446298.1, XM_017590809.1 [Q9WTL3-1]
XP_017446299.1, XM_017590810.1 [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

Similar proteinsi

Entry informationi

Entry nameiSEM6C_RAT
AccessioniPrimary (citable) accession number: Q9WTL3
Secondary accession number(s): Q9WTM6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: May 23, 2018
This is version 132 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health