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Protein

Semaphorin-6C

Gene

SEMA6C

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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: Ensembl
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:KIAA1869, SEMAY
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:10740. SEMA6C.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini25 – 604580ExtracellularSequence AnalysisAdd
BLAST
Transmembranei605 – 62521HelicalSequence AnalysisAdd
BLAST
Topological domaini626 – 930305CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

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

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

BgeeiQ9H3T2.
CleanExiHS_SEMA6C.
ExpressionAtlasiQ9H3T2. baseline and differential.
GenevestigatoriQ9H3T2.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000344148.

Structurei

3D structure databases

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

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.
GeneTreeiENSGT00760000119134.
HOVERGENiHBG072910.
InParanoidiQ9H3T2.
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. AlignAdd to basket

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

        10         20         30         40         50
MPRAPHFMPL LLLLLLLSLP HTQAAFPQDP LPLLISDLQG TSPLSWFRGL
60 70 80 90 100
EDDAVAAELG LDFQRFLTLN RTLLVAARDH VFSFDLQAEE EGEGLVPNKY
110 120 130 140 150
LTWRSQDVEN CAVRGKLTDE CYNYIRVLVP WDSQTLLACG TNSFSPVCRS
160 170 180 190 200
YGITSLQQEG EELSGQARCP FDATQSNVAI FAEGSLYSAT AADFQASDAV
210 220 230 240 250
VYRSLGPQPP LRSAKYDSKW LREPHFVQAL EHGDHVYFFF REVSVEDARL
260 270 280 290 300
GRVQFSRVAR VCKRDMGGSP RALDRHWTSF LKLRLNCSVP GDSTFYFDVL
310 320 330 340 350
QALTGPVNLH GRSALFGVFT TQTNSIPGSA VCAFYLDEIE RGFEGKFKEQ
360 370 380 390 400
RSLDGAWTPV SEDRVPSPRP GSCAGVGGAA LFSSSRDLPD DVLTFIKAHP
410 420 430 440 450
LLDPAVPPVT HQPLLTLTSR ALLTQVAVDG MAGPHSNITV MFLGSNDGTV
460 470 480 490 500
LKVLTPGGRS GGPEPILLEE IDAYSPARCS GKRTAQTARR IIGLELDTEG
510 520 530 540 550
HRLFVAFSGC IVYLPLSRCA RHGACQRSCL ASQDPYCGWH SSRGCVDIRG
560 570 580 590 600
SGGTDVDQAG NQESMEHGDC QDGATGSQSG PGDSAYGVRR DLPPASASRS
610 620 630 640 650
VPIPLLLASV AAAFALGASV SGLLVSCACR RAHRRRGKDI ETPGLPRPLS
660 670 680 690 700
LRSLARLHGG GPEPPPPSKD GDAVQTPQLY TTFLPPPEGV PPPELACLPT
710 720 730 740 750
PESTPELPVK HLRAAGDPWE WNQNRNNAKE GPGRSRGGHA AGGPAPRVLV
760 770 780 790 800
RPPPPGCPGQ AVEVTTLEEL LRYLHGPQPP RKGAEPPAPL TSRALPPEPA
810 820 830 840 850
PALLGGPSPR PHECASPLRL DVPPEGRCAS APARPALSAP APRLGVGGGR
860 870 880 890 900
RLPFSGHRAP PALLTRVPSG GPSRYSGGPG KHLLYLGRPE GYRGRALKRV
910 920 930
DVEKPQLSLK PPLVGPSSRQ AVPNGGRFNF
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.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti125 – 1251I → V in AAL72099 (PubMed:12110693).Curated
Sequence conflicti252 – 2521R → K in BAB20670 (Ref. 2) Curated

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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

STRINGi9606.ENSP00000344148.

PTM databases

PhosphoSiteiQ9H3T2.

Polymorphism databases

DMDMi313104318.

Proteomic databases

PaxDbiQ9H3T2.
PRIDEiQ9H3T2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi10500.
GeneCardsiGC01M151104.
HGNCiHGNC:10740. SEMA6C.
MIMi609294. gene.
neXtProtiNX_Q9H3T2.
PharmGKBiPA35662.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG293968.
GeneTreeiENSGT00760000119134.
HOVERGENiHBG072910.
InParanoidiQ9H3T2.
KOiK06842.
OMAiLVSCACR.
OrthoDBiEOG7SV0TJ.
PhylomeDBiQ9H3T2.
TreeFamiTF316102.

Miscellaneous databases

GeneWikiiSEMA6C.
GenomeRNAii10500.
NextBioi39844.
PROiQ9H3T2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9H3T2.
CleanExiHS_SEMA6C.
ExpressionAtlasiQ9H3T2. baseline and differential.
GenevestigatoriQ9H3T2.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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(2001) [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 (DEC-1998) 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(2000) [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(2005) [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: January 7, 2015
This is version 124 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.