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Protein

Semaphorin-4A

Gene

SEMA4A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Adaptive immunity, Angiogenesis, Differentiation, Immunity, Neurogenesis

Enzyme and pathway databases

BioCyciZFISH:G66-31930-MONOMER.
ReactomeiR-HSA-416700. Other semaphorin interactions.

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-4A
Alternative name(s):
Semaphorin-B
Short name:
Sema B
Gene namesi
Name:SEMA4A
Synonyms:SEMAB, SEMB
ORF Names:UNQ783/PRO1317
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:10729. SEMA4A.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini33 – 683ExtracellularSequence analysisAdd BLAST651
Transmembranei684 – 704HelicalSequence analysisAdd BLAST21
Topological domaini705 – 761CytoplasmicSequence analysisAdd BLAST57

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Involvement in diseasei

Retinitis pigmentosa 35 (RP35)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:610282
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_028322345D → H in RP35 and CORD10; heterozygous compound with C-350. 1 PublicationCorresponds to variant rs267607033dbSNPEnsembl.1
Natural variantiVAR_028323350F → C in RP35 and CORD10; heterozygous compound with H-345. 1 PublicationCorresponds to variant rs267607034dbSNPEnsembl.1
Natural variantiVAR_028325713R → Q in RP35; also in a patient with congenital blindness. 1 PublicationCorresponds to variant rs41265017dbSNPEnsembl.1
Cone-rod dystrophy 10 (CORD10)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn 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.
See also OMIM:610283
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_028322345D → H in RP35 and CORD10; heterozygous compound with C-350. 1 PublicationCorresponds to variant rs267607033dbSNPEnsembl.1
Natural variantiVAR_028323350F → C in RP35 and CORD10; heterozygous compound with H-345. 1 PublicationCorresponds to variant rs267607034dbSNPEnsembl.1

Keywords - Diseasei

Cone-rod dystrophy, Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi64218.
MalaCardsiSEMA4A.
MIMi610282. phenotype.
610283. phenotype.
OpenTargetsiENSG00000196189.
Orphaneti1872. Cone rod dystrophy.
791. Retinitis pigmentosa.
PharmGKBiPA35651.

Polymorphism and mutation databases

BioMutaiSEMA4A.
DMDMi29840871.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 32Sequence analysisAdd BLAST32
ChainiPRO_000003232233 – 761Semaphorin-4AAdd BLAST729

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi113 ↔ 124PROSITE-ProRule annotation
Glycosylationi120N-linked (GlcNAc...)Sequence analysis1
Glycosylationi135N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi142 ↔ 151PROSITE-ProRule annotation
Disulfide bondi269 ↔ 379PROSITE-ProRule annotation
Disulfide bondi293 ↔ 339PROSITE-ProRule annotation
Glycosylationi496N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi497 ↔ 514PROSITE-ProRule annotation
Disulfide bondi506 ↔ 523PROSITE-ProRule annotation
Disulfide bondi580 ↔ 624PROSITE-ProRule annotation
Glycosylationi607N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ9H3S1.
MaxQBiQ9H3S1.
PaxDbiQ9H3S1.
PeptideAtlasiQ9H3S1.
PRIDEiQ9H3S1.

PTM databases

iPTMnetiQ9H3S1.
PhosphoSitePlusiQ9H3S1.

Expressioni

Gene expression databases

BgeeiENSG00000196189.
CleanExiHS_SEMA4A.
ExpressionAtlasiQ9H3S1. baseline and differential.
GenevisibleiQ9H3S1. HS.

Organism-specific databases

HPAiHPA053726.
HPA066006.
HPA069136.

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
PLXND1Q9Y4D72EBI-3924922,EBI-310731

GO - Molecular functioni

Protein-protein interaction databases

BioGridi122108. 1 interactor.
IntActiQ9H3S1. 5 interactors.
MINTiMINT-4507832.
STRINGi9606.ENSP00000347117.

Structurei

3D structure databases

ProteinModelPortaliQ9H3S1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini36 – 494SemaPROSITE-ProRule annotationAdd BLAST459
Domaini496 – 548PSIAdd BLAST53
Domaini573 – 631Ig-like C2-typeAdd BLAST59

Sequence similaritiesi

Belongs to the semaphorin family.Curated
Contains 1 PSI domain.Curated
Contains 1 Sema domain.PROSITE-ProRule annotation

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061165.
InParanoidiQ9H3S1.
KOiK06521.
OMAiFAFSPAC.
OrthoDBiEOG091G01W0.
PhylomeDBiQ9H3S1.
TreeFamiTF316102.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR002165. Plexin_repeat.
IPR016201. PSI.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 2 hits.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
PROSITEiPS51004. SEMA. 1 hit.
[Graphical view]

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 1 (identifier: Q9H3S1-1) [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
MALPALGLDP WSLLGLFLFQ LLQLLLPTTT AGGGGQGPMP RVRYYAGDER
60 70 80 90 100
RALSFFHQKG LQDFDTLLLS GDGNTLYVGA REAILALDIQ DPGVPRLKNM
110 120 130 140 150
IPWPASDRKK SECAFKKKSN ETQCFNFIRV LVSYNVTHLY TCGTFAFSPA
160 170 180 190 200
CTFIELQDSY LLPISEDKVM EGKGQSPFDP AHKHTAVLVD GMLYSGTMNN
210 220 230 240 250
FLGSEPILMR TLGSQPVLKT DNFLRWLHHD ASFVAAIPST QVVYFFFEET
260 270 280 290 300
ASEFDFFERL HTSRVARVCK NDVGGEKLLQ KKWTTFLKAQ LLCTQPGQLP
310 320 330 340 350
FNVIRHAVLL PADSPTAPHI YAVFTSQWQV GGTRSSAVCA FSLLDIERVF
360 370 380 390 400
KGKYKELNKE TSRWTTYRGP ETNPRPGSCS VGPSSDKALT FMKDHFLMDE
410 420 430 440 450
QVVGTPLLVK SGVEYTRLAV ETAQGLDGHS HLVMYLGTTT GSLHKAVVSG
460 470 480 490 500
DSSAHLVEEI QLFPDPEPVR NLQLAPTQGA VFVGFSGGVW RVPRANCSVY
510 520 530 540 550
ESCVDCVLAR DPHCAWDPES RTCCLLSAPN LNSWKQDMER GNPEWACASG
560 570 580 590 600
PMSRSLRPQS RPQIIKEVLA VPNSILELPC PHLSALASYY WSHGPAAVPE
610 620 630 640 650
ASSTVYNGSL LLIVQDGVGG LYQCWATENG FSYPVISYWV DSQDQTLALD
660 670 680 690 700
PELAGIPREH VKVPLTRVSG GAALAAQQSY WPHFVTVTVL FALVLSGALI
710 720 730 740 750
ILVASPLRAL RARGKVQGCE TLRPGEKAPL SREQHLQSPK ECRTSASDVD
760
ADNNCLGTEV A
Length:761
Mass (Da):83,574
Last modified:April 11, 2003 - v2
Checksum:i5BCB889AA32A2BB3
GO
Isoform 2 (identifier: Q9H3S1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-99: Missing.
     122-154: Missing.

Note: No experimental confirmation available.
Show »
Length:629
Mass (Da):69,104
Checksum:i3B97BA202D33502B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti293 – 328CTQPG…FTSQW → SAPSRGSCPSTSSATRSCSP PILPQLPTSTQSSPPSG (Ref. 1) CuratedAdd BLAST36
Sequence conflicti354Y → F in BAB20087 (Ref. 1) Curated1
Sequence conflicti641D → G in BAG52288 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_028322345D → H in RP35 and CORD10; heterozygous compound with C-350. 1 PublicationCorresponds to variant rs267607033dbSNPEnsembl.1
Natural variantiVAR_028323350F → C in RP35 and CORD10; heterozygous compound with H-345. 1 PublicationCorresponds to variant rs267607034dbSNPEnsembl.1
Natural variantiVAR_028324510R → Q.Corresponds to variant rs2075164dbSNPEnsembl.1
Natural variantiVAR_028325713R → Q in RP35; also in a patient with congenital blindness. 1 PublicationCorresponds to variant rs41265017dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0463811 – 99Missing in isoform 2. 1 PublicationAdd BLAST99
Alternative sequenceiVSP_046382122 – 154Missing in isoform 2. 1 PublicationAdd BLAST33

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS1132.1. [Q9H3S1-1]
CCDS53378.1. [Q9H3S1-2]
RefSeqiNP_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]
XP_011508174.1. XM_011509872.2. [Q9H3S1-1]
XP_011508175.1. XM_011509873.2. [Q9H3S1-1]
XP_016857545.1. XM_017002056.1. [Q9H3S1-1]
UniGeneiHs.408846.

Genome annotation databases

EnsembliENST00000355014; ENSP00000347117; ENSG00000196189. [Q9H3S1-1]
ENST00000368282; ENSP00000357265; ENSG00000196189. [Q9H3S1-1]
ENST00000368284; ENSP00000357267; ENSG00000196189. [Q9H3S1-2]
ENST00000368285; ENSP00000357268; ENSG00000196189. [Q9H3S1-1]
GeneIDi64218.
KEGGihsa:64218.
UCSCiuc001fnl.4. human. [Q9H3S1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS1132.1. [Q9H3S1-1]
CCDS53378.1. [Q9H3S1-2]
RefSeqiNP_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]
XP_011508174.1. XM_011509872.2. [Q9H3S1-1]
XP_011508175.1. XM_011509873.2. [Q9H3S1-1]
XP_016857545.1. XM_017002056.1. [Q9H3S1-1]
UniGeneiHs.408846.

3D structure databases

ProteinModelPortaliQ9H3S1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122108. 1 interactor.
IntActiQ9H3S1. 5 interactors.
MINTiMINT-4507832.
STRINGi9606.ENSP00000347117.

PTM databases

iPTMnetiQ9H3S1.
PhosphoSitePlusiQ9H3S1.

Polymorphism and mutation databases

BioMutaiSEMA4A.
DMDMi29840871.

Proteomic databases

EPDiQ9H3S1.
MaxQBiQ9H3S1.
PaxDbiQ9H3S1.
PeptideAtlasiQ9H3S1.
PRIDEiQ9H3S1.

Protocols and materials databases

DNASUi64218.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000355014; ENSP00000347117; ENSG00000196189. [Q9H3S1-1]
ENST00000368282; ENSP00000357265; ENSG00000196189. [Q9H3S1-1]
ENST00000368284; ENSP00000357267; ENSG00000196189. [Q9H3S1-2]
ENST00000368285; ENSP00000357268; ENSG00000196189. [Q9H3S1-1]
GeneIDi64218.
KEGGihsa:64218.
UCSCiuc001fnl.4. human. [Q9H3S1-1]

Organism-specific databases

CTDi64218.
DisGeNETi64218.
GeneCardsiSEMA4A.
GeneReviewsiSEMA4A.
HGNCiHGNC:10729. SEMA4A.
HPAiHPA053726.
HPA066006.
HPA069136.
MalaCardsiSEMA4A.
MIMi607292. gene.
610282. phenotype.
610283. phenotype.
neXtProtiNX_Q9H3S1.
OpenTargetsiENSG00000196189.
Orphaneti1872. Cone rod dystrophy.
791. Retinitis pigmentosa.
PharmGKBiPA35651.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061165.
InParanoidiQ9H3S1.
KOiK06521.
OMAiFAFSPAC.
OrthoDBiEOG091G01W0.
PhylomeDBiQ9H3S1.
TreeFamiTF316102.

Enzyme and pathway databases

BioCyciZFISH:G66-31930-MONOMER.
ReactomeiR-HSA-416700. Other semaphorin interactions.

Miscellaneous databases

ChiTaRSiSEMA4A. human.
GeneWikiiSEMA4A.
GenomeRNAii64218.
PROiQ9H3S1.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000196189.
CleanExiHS_SEMA4A.
ExpressionAtlasiQ9H3S1. baseline and differential.
GenevisibleiQ9H3S1. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR002165. Plexin_repeat.
IPR016201. PSI.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 2 hits.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
PROSITEiPS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSEM4A_HUMAN
AccessioniPrimary (citable) accession number: Q9H3S1
Secondary accession number(s): B2RDH8
, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: April 11, 2003
Last modified: November 30, 2016
This is version 151 of the entry and version 2 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

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 one 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.