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Q8NFY4 (SEM6D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 100. 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-6D
Gene names
Name:SEMA6D
Synonyms:KIAA1479
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1073 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.

Subcellular location

Isoform 1: Cell membrane; Single-pass type I membrane protein Ref.1.

Isoform 2: Cell membrane; Single-pass type I membrane protein Ref.1.

Isoform 3: Cell membrane; Single-pass type I membrane protein Ref.1.

Isoform 4: Cell membrane; Single-pass type I membrane protein Ref.1.

Isoform 5: Cell membrane; Single-pass type I membrane protein Ref.1.

Isoform 7: Cytoplasm Ref.1.

Sequence similarities

Belongs to the semaphorin family.

Contains 1 PSI domain.

Contains 1 Sema domain.

Sequence caution

The sequence BAA96003.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Alternative products

This entry describes 8 isoforms produced by alternative splicing. [Align] [Select]
Isoform 4 (identifier: Q8NFY4-1)

Also known as: SEMA6D.4;

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 1 (identifier: Q8NFY4-2)

Also known as: SEMA6D.1;

The sequence of this isoform differs from the canonical sequence as follows:
     549-549: L → LLLTEDFFAFHNHS
     570-644: Missing.
Isoform 2 (identifier: Q8NFY4-3)

Also known as: SEMA6D.2;

The sequence of this isoform differs from the canonical sequence as follows:
     570-644: Missing.
Isoform 3 (identifier: Q8NFY4-4)

Also known as: SEMA6D.3;

The sequence of this isoform differs from the canonical sequence as follows:
     589-644: Missing.
Isoform 5 (identifier: Q8NFY4-5)

The sequence of this isoform differs from the canonical sequence as follows:
     549-549: L → LLLTEDFFAFHNHS
     589-644: Missing.
Note: No experimental confirmation available.
Isoform 6 (identifier: Q8NFY4-6)

The sequence of this isoform differs from the canonical sequence as follows:
     570-588: Missing.
Note: No experimental confirmation available.
Isoform 7 (identifier: Q8NFY4-7)

Also known as: SEMA6Ds; Short;

The sequence of this isoform differs from the canonical sequence as follows:
     477-1073: Missing.
Isoform 8 (identifier: Q8NFY4-8)

The sequence of this isoform differs from the canonical sequence as follows:
     570-588: Missing.
     601-1073: ASIPEITPKV...SVRPLNKYTY → VYDGKSSLESPTRWST
Note: No experimental confirmation available. Gene prediction based on mRNA data.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2020 Potential
Chain21 – 10731053Semaphorin-6D
PRO_0000044615

Regions

Topological domain21 – 662642Extracellular Potential
Transmembrane663 – 68321Helical; Potential
Topological domain684 – 1073390Cytoplasmic Potential
Domain27 – 512486Sema
Domain514 – 56956PSI

Amino acid modifications

Glycosylation511N-linked (GlcNAc...) Potential
Glycosylation2831N-linked (GlcNAc...) Potential
Glycosylation4351N-linked (GlcNAc...) Potential
Glycosylation4611N-linked (GlcNAc...) Potential
Glycosylation6311N-linked (GlcNAc...) Potential
Disulfide bond108 ↔ 118 By similarity
Disulfide bond136 ↔ 145 By similarity
Disulfide bond259 ↔ 370 By similarity
Disulfide bond284 ↔ 329 By similarity
Disulfide bond477 ↔ 506 By similarity
Disulfide bond515 ↔ 533 By similarity
Disulfide bond521 ↔ 568 By similarity
Disulfide bond525 ↔ 541 By similarity

Natural variations

Alternative sequence477 – 1073597Missing in isoform 7.
VSP_016564
Alternative sequence5491L → LLLTEDFFAFHNHS in isoform 1 and isoform 5.
VSP_016565
Alternative sequence570 – 64475Missing in isoform 1 and isoform 2.
VSP_016566
Alternative sequence570 – 58819Missing in isoform 6 and isoform 8.
VSP_016572
Alternative sequence589 – 64456Missing in isoform 3 and isoform 5.
VSP_016567
Alternative sequence601 – 1073473ASIPE…NKYTY → VYDGKSSLESPTRWST in isoform 8.
VSP_054084
Natural variant3071N → S.
Corresponds to variant rs3743279 [ dbSNP | Ensembl ].
VAR_051931
Natural variant4781S → N.
Corresponds to variant rs532598 [ dbSNP | Ensembl ].
VAR_051932
Natural variant9691S → T.
Corresponds to variant rs16960074 [ dbSNP | Ensembl ].
VAR_051933

Sequences

Sequence LengthMass (Da)Tools
Isoform 4 (SEMA6D.4) [UniParc].

Last modified October 1, 2002. Version 1.
Checksum: 7DCE4DFC5BF70F9E

FASTA1,073119,872
        10         20         30         40         50         60 
MRVFLLCAYI LLLMVSQLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ 

        70         80         90        100        110        120 
LMLKIRDTLY IAGRDQVYTV NLNEMPKTEV IPNKKLTWRS RQQDRENCAM KGKHKDECHN 

       130        140        150        160        170        180 
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL STLEYDGEEI SGLARCPFDA RQTNVALFAD 

       190        200        210        220        230        240 
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI 

       250        260        270        280        290        300 
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI 

       310        320        330        340        350        360 
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED 

       370        380        390        400        410        420 
KVPKPRPGCC AKHGLAEAYK TSIDFPDETL SFIKSHPLMD SAVPPIADEP WFTKTRVRYR 

       430        440        450        460        470        480 
LTAISVDHSA GPYQNYTVIF VGSEAGMVLK VLAKTSPFSL NDSVLLEEIE AYNHAKCSAE 

       490        500        510        520        530        540 
NEEDKKVISL QLDKDHHALY VAFSSCIIRI PLSRCERYGS CKKSCIASRD PYCGWLSQGS 

       550        560        570        580        590        600 
CGRVTPGMLA EGYEQDTEFG NTAHLGDCHE ILPTSTTPDY KIFGGPTSDM EVSSSSVTTM 

       610        620        630        640        650        660 
ASIPEITPKV IDTWRPKLTS SRKFVVQDDP NTSDFTDPLS GIPKGVRWEV QSGESNQMVH 

       670        680        690        700        710        720 
MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL 

       730        740        750        760        770        780 
FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NGDTKSMVMD HRGQPPELAA LPTPESTPVL 

       790        800        810        820        830        840 
HQKTLQAMKS HSEKAHGHGA SRKETPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS 

       850        860        870        880        890        900 
FSNSNAHKAE KKLQNIDHPL TKSSSKRDHR RSVDSRNTLN DLLKHLNDPN SNPKAIMGDI 

       910        920        930        940        950        960 
QMAHQNLMLD PMGSMSEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER 

       970        980        990       1000       1010       1020 
QRGYHKNSSQ RHSISAMPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH 

      1030       1040       1050       1060       1070 
LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTPSVRPLNK YTY 

« Hide

Isoform 1 (SEMA6D.1) [UniParc].

Checksum: 9D6B8B3633941B89
Show »

FASTA1,011113,290
Isoform 2 (SEMA6D.2) [UniParc].

Checksum: 3F46D6872E8D5344
Show »

FASTA998111,730
Isoform 3 (SEMA6D.3) [UniParc].

Checksum: 4D639CEBADD9F2A0
Show »

FASTA1,017113,736
Isoform 5 [UniParc].

Checksum: 659CF8EA114B048F
Show »

FASTA1,030115,296
Isoform 6 [UniParc].

Checksum: A888C403FFACEE8F
Show »

FASTA1,054117,866
Isoform 7 (SEMA6Ds) (Short) [UniParc].

Checksum: 3AAB6E77051D2D83
Show »

FASTA47654,217
Isoform 8 [UniParc].

Checksum: 58D3EE7B6B68DB67
Show »

FASTA59767,538

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; 3; 4 AND 7), SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
Tissue: Brain.
[2]"Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.
DNA Res. 7:143-150(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Brain.
[3]"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION.
[4]"Analysis of the DNA sequence and duplication history of human chromosome 15."
Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A. expand/collapse author list , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF389426 mRNA. Translation: AAM69449.1.
AF389427 mRNA. Translation: AAM69450.1.
AF389428 mRNA. Translation: AAM69451.1.
AF389429 mRNA. Translation: AAM69452.1.
AF389430 mRNA. Translation: AAM69453.1.
AB040912 mRNA. Translation: BAA96003.2. Different initiation.
AC018900 Genomic DNA. No translation available.
AC044787 Genomic DNA. No translation available.
AC009558 Genomic DNA. No translation available.
AC012050 Genomic DNA. No translation available.
AC023905 Genomic DNA. No translation available.
AC066615 Genomic DNA. No translation available.
AC084882 Genomic DNA. No translation available.
BC150253 mRNA. Translation: AAI50254.1.
CCDSCCDS32224.1. [Q8NFY4-2]
CCDS32225.1. [Q8NFY4-1]
CCDS32226.1. [Q8NFY4-4]
CCDS32227.1. [Q8NFY4-3]
CCDS32229.1. [Q8NFY4-7]
RefSeqNP_001185928.1. NM_001198999.1. [Q8NFY4-2]
NP_065909.1. NM_020858.1. [Q8NFY4-2]
NP_079242.2. NM_024966.2. [Q8NFY4-7]
NP_705869.1. NM_153616.1. [Q8NFY4-3]
NP_705870.1. NM_153617.1. [Q8NFY4-4]
NP_705871.1. NM_153618.1. [Q8NFY4-1]
NP_705872.1. NM_153619.1. [Q8NFY4-8]
XP_005254744.1. XM_005254687.1. [Q8NFY4-1]
XP_005254746.1. XM_005254689.1. [Q8NFY4-6]
XP_005254747.1. XM_005254690.1. [Q8NFY4-5]
UniGeneHs.511265.

3D structure databases

ProteinModelPortalQ8NFY4.
SMRQ8NFY4. Positions 23-533.
ModBaseSearch...
MobiDBSearch...

PTM databases

PhosphoSiteQ8NFY4.

Polymorphism databases

DMDM74715611.

Proteomic databases

MaxQBQ8NFY4.
PaxDbQ8NFY4.
PRIDEQ8NFY4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000316364; ENSP00000324857; ENSG00000137872. [Q8NFY4-1]
ENST00000354744; ENSP00000346786; ENSG00000137872. [Q8NFY4-4]
ENST00000355997; ENSP00000348276; ENSG00000137872.
ENST00000358066; ENSP00000350770; ENSG00000137872. [Q8NFY4-2]
ENST00000389425; ENSP00000374076; ENSG00000137872. [Q8NFY4-7]
ENST00000389428; ENSP00000374079; ENSG00000137872. [Q8NFY4-3]
ENST00000389432; ENSP00000374083; ENSG00000137872. [Q8NFY4-5]
ENST00000389433; ENSP00000374084; ENSG00000137872. [Q8NFY4-6]
ENST00000536845; ENSP00000446152; ENSG00000137872. [Q8NFY4-1]
ENST00000537942; ENSP00000442040; ENSG00000137872. [Q8NFY4-2]
ENST00000558014; ENSP00000452815; ENSG00000137872. [Q8NFY4-2]
ENST00000558816; ENSP00000453661; ENSG00000137872.
GeneID80031.
KEGGhsa:80031.
UCSCuc001zvw.3. human. [Q8NFY4-2]
uc001zvx.1. human. [Q8NFY4-7]
uc001zvy.3. human. [Q8NFY4-1]
uc001zvz.3. human. [Q8NFY4-4]
uc001zwc.3. human. [Q8NFY4-3]

Organism-specific databases

CTD80031.
GeneCardsGC15P047476.
HGNCHGNC:16770. SEMA6D.
HPAHPA043109.
MIM609295. gene.
neXtProtNX_Q8NFY4.
PharmGKBPA134951035.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG293968.
HOGENOMHOG000232047.
HOVERGENHBG072910.
InParanoidQ8NFY4.
KOK06842.
OMACVFAAFV.
OrthoDBEOG7SV0TJ.
PhylomeDBQ8NFY4.
TreeFamTF316102.

Enzyme and pathway databases

ReactomeREACT_111045. Developmental Biology.

Gene expression databases

ArrayExpressQ8NFY4.
BgeeQ8NFY4.
GenevestigatorQ8NFY4.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR016201. Plexin-like_fold.
IPR002165. Plexin_repeat.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERPTHR11036. PTHR11036. 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

GenomeRNAi80031.
NextBio70190.
PROQ8NFY4.
SOURCESearch...

Entry information

Entry nameSEM6D_HUMAN
AccessionPrimary (citable) accession number: Q8NFY4
Secondary accession number(s): A6NF10 expand/collapse secondary AC list , A6NM95, A6NNK1, A7E2A0, Q8NFY3, Q8NFY5, Q8NFY6, Q8NFY7, Q9P249
Entry history
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: October 1, 2002
Last modified: July 9, 2014
This is version 100 of the entry and version 1 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 15

Human chromosome 15: entries, gene names and cross-references to MIM