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Q9H3S1 (SEM4A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 129. 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·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Semaphorin-4A
Alternative name(s):
Semaphorin-B
Short name=Sema B
Gene names
Name:SEMA4A
Synonyms:SEMAB, SEMB
ORF Names:UNQ783/PRO1317
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length761 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Cell surface receptor for PLXNB1, PLXNB2, PLXNB3 and PLXND1 that plays an important role in cell-cell signaling. Plays a role in priming antigen-specific T-cells, promotes differentiation of Th1 T-helper cells, and thereby contributes to adaptive immunity. Promotes phosphorylation of TIMD2. Inhibits angiogenesis. Promotes axon growth cone collapse. Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons By similarity.

Subunit structure

Interacts with PLXNB1, PLXNB2, PLXNB3 and PLXND1. Probable ligand for TIMD2 By similarity.

Subcellular location

Cell membrane; Single-pass type I membrane protein By similarity.

Involvement in disease

Retinitis pigmentosa 35 (RP35) [MIM:610282]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.6

Cone-rod dystrophy 10 (CORD10) [MIM:610283]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.6

Sequence similarities

Belongs to the semaphorin family.

Contains 1 Ig-like C2-type (immunoglobulin-like) domain.

Contains 1 PSI domain.

Contains 1 Sema domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PLXND1Q9Y4D72EBI-3924922,EBI-310731

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H3S1-1)

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: Q9H3S1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-99: Missing.
     122-154: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3232 Potential
Chain33 – 761729Semaphorin-4A
PRO_0000032322

Regions

Topological domain33 – 683651Extracellular Potential
Transmembrane684 – 70421Helical; Potential
Topological domain705 – 76157Cytoplasmic Potential
Domain36 – 494459Sema
Domain496 – 54853PSI
Domain573 – 63159Ig-like C2-type

Amino acid modifications

Glycosylation1201N-linked (GlcNAc...) Potential
Glycosylation1351N-linked (GlcNAc...) Potential
Glycosylation4961N-linked (GlcNAc...) Potential
Glycosylation6071N-linked (GlcNAc...) Potential
Disulfide bond113 ↔ 124 By similarity
Disulfide bond142 ↔ 151 By similarity
Disulfide bond269 ↔ 379 By similarity
Disulfide bond293 ↔ 339 By similarity
Disulfide bond497 ↔ 514 By similarity
Disulfide bond506 ↔ 523 By similarity
Disulfide bond580 ↔ 624 By similarity

Natural variations

Alternative sequence1 – 9999Missing in isoform 2.
VSP_046381
Alternative sequence122 – 15433Missing in isoform 2.
VSP_046382
Natural variant3451D → H in RP35 and CORD10; heterozygous compound with C-350. Ref.6
VAR_028322
Natural variant3501F → C in RP35 and CORD10; heterozygous compound with H-345. Ref.6
VAR_028323
Natural variant5101R → Q.
Corresponds to variant rs2075164 [ dbSNP | Ensembl ].
VAR_028324
Natural variant7131R → Q in RP35; also in a patient with congenital blindness. Ref.6
Corresponds to variant rs41265017 [ dbSNP | Ensembl ].
VAR_028325

Experimental info

Sequence conflict293 – 32836CTQPG…FTSQW → SAPSRGSCPSTSSATRSCSP PILPQLPTSTQSSPPSG Ref.1
Sequence conflict3541Y → F in BAB20087. Ref.1
Sequence conflict6411D → G in BAG52288. Ref.3

Sequences

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

Last modified April 11, 2003. Version 2.
Checksum: 5BCB889AA32A2BB3

FASTA76183,574
        10         20         30         40         50         60 
MALPALGLDP WSLLGLFLFQ LLQLLLPTTT AGGGGQGPMP RVRYYAGDER RALSFFHQKG 

        70         80         90        100        110        120 
LQDFDTLLLS GDGNTLYVGA REAILALDIQ DPGVPRLKNM IPWPASDRKK SECAFKKKSN 

       130        140        150        160        170        180 
ETQCFNFIRV LVSYNVTHLY TCGTFAFSPA CTFIELQDSY LLPISEDKVM EGKGQSPFDP 

       190        200        210        220        230        240 
AHKHTAVLVD GMLYSGTMNN FLGSEPILMR TLGSQPVLKT DNFLRWLHHD ASFVAAIPST 

       250        260        270        280        290        300 
QVVYFFFEET ASEFDFFERL HTSRVARVCK NDVGGEKLLQ KKWTTFLKAQ LLCTQPGQLP 

       310        320        330        340        350        360 
FNVIRHAVLL PADSPTAPHI YAVFTSQWQV GGTRSSAVCA FSLLDIERVF KGKYKELNKE 

       370        380        390        400        410        420 
TSRWTTYRGP ETNPRPGSCS VGPSSDKALT FMKDHFLMDE QVVGTPLLVK SGVEYTRLAV 

       430        440        450        460        470        480 
ETAQGLDGHS HLVMYLGTTT GSLHKAVVSG DSSAHLVEEI QLFPDPEPVR NLQLAPTQGA 

       490        500        510        520        530        540 
VFVGFSGGVW RVPRANCSVY ESCVDCVLAR DPHCAWDPES RTCCLLSAPN LNSWKQDMER 

       550        560        570        580        590        600 
GNPEWACASG PMSRSLRPQS RPQIIKEVLA VPNSILELPC PHLSALASYY WSHGPAAVPE 

       610        620        630        640        650        660 
ASSTVYNGSL LLIVQDGVGG LYQCWATENG FSYPVISYWV DSQDQTLALD PELAGIPREH 

       670        680        690        700        710        720 
VKVPLTRVSG GAALAAQQSY WPHFVTVTVL FALVLSGALI ILVASPLRAL RARGKVQGCE 

       730        740        750        760 
TLRPGEKAPL SREQHLQSPK ECRTSASDVD ADNNCLGTEV A 

« Hide

Isoform 2 [UniParc].

Checksum: 3B97BA202D33502B
Show »

FASTA62969,104

References

« Hide 'large scale' references
[1]"Human semaphorin B."
Seki N., Hattori A., Hayashi A., Kozuma S., Muramatsu M., Miyajima N., Saito T.
Submitted (JUN-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment."
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. expand/collapse author list , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.
Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Placenta and Tongue.
[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]"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).
Tissue: Colon.
[6]"Identification of novel mutations in the SEMA4A gene associated with retinal degenerative diseases."
Abid A., Ismail M., Mehdi S.Q., Khaliq S.
J. Med. Genet. 43:378-381(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS RP35 HIS-345; CYS-350 AND GLN-713, VARIANTS CORD10 HIS-345 AND CYS-350.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB029394 mRNA. Translation: BAB20087.1.
AY358531 mRNA. Translation: AAQ88895.1.
AK091127 mRNA. Translation: BAG52288.1.
AK315547 mRNA. Translation: BAG37925.1.
AL135927 Genomic DNA. Translation: CAI15530.1.
AL135927 Genomic DNA. Translation: CAI15533.1.
BC020974 mRNA. Translation: AAH20974.1.
CCDSCCDS1132.1. [Q9H3S1-1]
CCDS53378.1. [Q9H3S1-2]
RefSeqNP_001180229.1. NM_001193300.1. [Q9H3S1-1]
NP_001180230.1. NM_001193301.1. [Q9H3S1-1]
NP_001180231.1. NM_001193302.1. [Q9H3S1-2]
NP_071762.2. NM_022367.3. [Q9H3S1-1]
UniGeneHs.408846.

3D structure databases

ProteinModelPortalQ9H3S1.
SMRQ9H3S1. Positions 37-628.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid122108. 1 interaction.
IntActQ9H3S1. 5 interactions.
MINTMINT-4507832.
STRING9606.ENSP00000347117.

PTM databases

PhosphoSiteQ9H3S1.

Polymorphism databases

DMDM29840871.

Proteomic databases

MaxQBQ9H3S1.
PaxDbQ9H3S1.
PRIDEQ9H3S1.

Protocols and materials databases

DNASU64218.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000355014; ENSP00000347117; ENSG00000196189. [Q9H3S1-1]
ENST00000368282; ENSP00000357265; ENSG00000196189. [Q9H3S1-1]
ENST00000368284; ENSP00000357267; ENSG00000196189. [Q9H3S1-2]
ENST00000368285; ENSP00000357268; ENSG00000196189. [Q9H3S1-1]
ENST00000368286; ENSP00000357269; ENSG00000196189. [Q9H3S1-2]
GeneID64218.
KEGGhsa:64218.
UCSCuc001fnl.3. human. [Q9H3S1-1]
uc001fnn.3. human.

Organism-specific databases

CTD64218.
GeneCardsGC01P156119.
GeneReviewsSEMA4A.
HGNCHGNC:10729. SEMA4A.
MIM607292. gene.
610282. phenotype.
610283. phenotype.
neXtProtNX_Q9H3S1.
Orphanet1872. Cone rod dystrophy.
791. Retinitis pigmentosa.
PharmGKBPA35651.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG287504.
HOGENOMHOG000116087.
HOVERGENHBG061165.
InParanoidQ9H3S1.
KOK06521.
OMAFAFSPAC.
OrthoDBEOG7H791Q.
PhylomeDBQ9H3S1.
TreeFamTF316102.

Enzyme and pathway databases

ReactomeREACT_111045. Developmental Biology.

Gene expression databases

ArrayExpressQ9H3S1.
BgeeQ9H3S1.
CleanExHS_SEMA4A.
GenevestigatorQ9H3S1.

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

GeneWikiSEMA4A.
GenomeRNAi64218.
NextBio66131.
PROQ9H3S1.
SOURCESearch...

Entry information

Entry nameSEM4A_HUMAN
AccessionPrimary (citable) accession number: Q9H3S1
Secondary accession number(s): B2RDH8 expand/collapse secondary AC list , B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9
Entry history
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: April 11, 2003
Last modified: July 9, 2014
This is version 129 of the entry and version 2 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