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Q9H3T2 (SEM6C_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | 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:KIAA1869, SEMAY
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length930 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

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

Sequence similarities

Belongs to the semaphorin family.

Contains 1 PSI domain.

Contains 1 Sema domain.

Sequence caution

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

Ontologies

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

Inferred from electronic annotation. Source: Ensembl

   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 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H3T2-1)

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.
Isoform 2 (identifier: Q9H3T2-2)

Also known as: Short 2;

The sequence of this isoform differs from the canonical sequence as follows:
     184-223: Missing.
     586-586: Y → YVLPGPGPSPGTPSPPSDAHPRPQSSTLGVHTR
Isoform 3 (identifier: Q9H3T2-3)

Also known as: Long;

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2424 Potential
Chain25 – 930906Semaphorin-6C
PRO_0000032344

Regions

Topological domain25 – 604580Extracellular Potential
Transmembrane605 – 62521Helical; Potential
Topological domain626 – 930305Cytoplasmic Potential
Domain30 – 516487Sema
Compositional bias662 – 6676Poly-Pro
Compositional bias752 – 7554Poly-Pro

Amino acid modifications

Glycosylation701N-linked (GlcNAc...) Potential
Glycosylation2861N-linked (GlcNAc...) Potential
Glycosylation4371N-linked (GlcNAc...) Potential
Disulfide bond111 ↔ 121 By similarity
Disulfide bond139 ↔ 148 By similarity
Disulfide bond262 ↔ 373 By similarity
Disulfide bond287 ↔ 332 By similarity
Disulfide bond479 ↔ 510 By similarity
Disulfide bond519 ↔ 537 By similarity
Disulfide bond525 ↔ 570 By similarity
Disulfide bond529 ↔ 545 By similarity

Natural variations

Alternative sequence184 – 22340Missing in isoform 2.
VSP_006046
Alternative sequence5861Y → YVLPGPGPSPGTPSPPSDAH PRPQSSTLGVHTR in isoform 2 and isoform 3.
VSP_006047
Natural variant4551T → P. Ref.1 Ref.5
Corresponds to variant rs4971007 [ dbSNP | Ensembl ].
VAR_028144

Experimental info

Sequence conflict1251I → V in AAL72099. Ref.1
Sequence conflict2521R → K in BAB20670. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Short 1) [UniParc].

Last modified November 30, 2010. Version 4.
Checksum: 05C2D84413208640

FASTA93099,686
        10         20         30         40         50         60 
MPRAPHFMPL LLLLLLLSLP HTQAAFPQDP LPLLISDLQG TSPLSWFRGL EDDAVAAELG 

        70         80         90        100        110        120 
LDFQRFLTLN RTLLVAARDH VFSFDLQAEE EGEGLVPNKY LTWRSQDVEN CAVRGKLTDE 

       130        140        150        160        170        180 
CYNYIRVLVP WDSQTLLACG TNSFSPVCRS YGITSLQQEG EELSGQARCP FDATQSNVAI 

       190        200        210        220        230        240 
FAEGSLYSAT AADFQASDAV VYRSLGPQPP LRSAKYDSKW LREPHFVQAL EHGDHVYFFF 

       250        260        270        280        290        300 
REVSVEDARL GRVQFSRVAR VCKRDMGGSP RALDRHWTSF LKLRLNCSVP GDSTFYFDVL 

       310        320        330        340        350        360 
QALTGPVNLH GRSALFGVFT TQTNSIPGSA VCAFYLDEIE RGFEGKFKEQ RSLDGAWTPV 

       370        380        390        400        410        420 
SEDRVPSPRP GSCAGVGGAA LFSSSRDLPD DVLTFIKAHP LLDPAVPPVT HQPLLTLTSR 

       430        440        450        460        470        480 
ALLTQVAVDG MAGPHSNITV MFLGSNDGTV LKVLTPGGRS GGPEPILLEE IDAYSPARCS 

       490        500        510        520        530        540 
GKRTAQTARR IIGLELDTEG HRLFVAFSGC IVYLPLSRCA RHGACQRSCL ASQDPYCGWH 

       550        560        570        580        590        600 
SSRGCVDIRG SGGTDVDQAG NQESMEHGDC QDGATGSQSG PGDSAYGVRR DLPPASASRS 

       610        620        630        640        650        660 
VPIPLLLASV AAAFALGASV SGLLVSCACR RAHRRRGKDI ETPGLPRPLS LRSLARLHGG 

       670        680        690        700        710        720 
GPEPPPPSKD GDAVQTPQLY TTFLPPPEGV PPPELACLPT PESTPELPVK HLRAAGDPWE 

       730        740        750        760        770        780 
WNQNRNNAKE GPGRSRGGHA AGGPAPRVLV RPPPPGCPGQ AVEVTTLEEL LRYLHGPQPP 

       790        800        810        820        830        840 
RKGAEPPAPL TSRALPPEPA PALLGGPSPR PHECASPLRL DVPPEGRCAS APARPALSAP 

       850        860        870        880        890        900 
APRLGVGGGR RLPFSGHRAP PALLTRVPSG GPSRYSGGPG KHLLYLGRPE GYRGRALKRV 

       910        920        930 
DVEKPQLSLK PPLVGPSSRQ AVPNGGRFNF 

« Hide

Isoform 2 (Short 2) [UniParc].

Checksum: 8C201728A8F12530
Show »

FASTA92298,468
Isoform 3 (Long) [UniParc].

Checksum: 2A6B60559BB873E4
Show »

FASTA962102,853

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT PRO-455.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001171532.1. NM_001178061.1.
NP_001171533.1. NM_001178062.1.
NP_112175.2. NM_030913.4.
XP_005244890.1. XM_005244833.1.
XP_005244892.1. XM_005244835.1.
XP_005244893.1. XM_005244836.1.
UniGeneHs.516316.

3D structure databases

ProteinModelPortalQ9H3T2.
SMRQ9H3T2. Positions 26-544.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000344148.

PTM databases

PhosphoSiteQ9H3T2.

Polymorphism databases

DMDM313104318.

Proteomic databases

PaxDbQ9H3T2.
PRIDEQ9H3T2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000341697; ENSP00000344148; ENSG00000143434. [Q9H3T2-1]
ENST00000368912; ENSP00000357908; ENSG00000143434. [Q9H3T2-2]
ENST00000368913; ENSP00000357909; ENSG00000143434. [Q9H3T2-3]
ENST00000368914; ENSP00000357910; ENSG00000143434. [Q9H3T2-1]
GeneID10500.
KEGGhsa:10500.
UCSCuc001ewu.3. human. [Q9H3T2-1]
uc001ewv.3. human. [Q9H3T2-3]
uc001eww.3. human. [Q9H3T2-2]

Organism-specific databases

CTD10500.
GeneCardsGC01M151104.
HGNCHGNC:10740. SEMA6C.
MIM609294. gene.
neXtProtNX_Q9H3T2.
PharmGKBPA35662.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG293968.
HOVERGENHBG072910.
KOK06842.
OMALVSCACR.
OrthoDBEOG7SV0TJ.
PhylomeDBQ9H3T2.
TreeFamTF316102.

Gene expression databases

ArrayExpressQ9H3T2.
BgeeQ9H3T2.
CleanExHS_SEMA6C.
GenevestigatorQ9H3T2.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR016201. Plexin-like_fold.
IPR002165. Plexin_repeat.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015514. Semaphorin_6C.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERPTHR11036. PTHR11036. 1 hit.
PTHR11036:SF9. PTHR11036:SF9. 1 hit.
PfamPF01437. PSI. 1 hit.
PF01403. 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

GeneWikiSEMA6C.
GenomeRNAi10500.
NextBio39844.
PROQ9H3T2.
SOURCESearch...

Entry information

Entry nameSEM6C_HUMAN
AccessionPrimary (citable) accession number: Q9H3T2
Secondary accession number(s): D3DV15 expand/collapse secondary AC list , Q5JR71, Q5JR72, Q5JR73, Q8WXT8, Q8WXT9, Q8WXU0, Q96JF8
Entry history
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 30, 2010
Last modified: April 16, 2014
This is version 118 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM