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Protein

Semaphorin-3A

Gene

Sema3a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a role in growth cones guidance. May function to pattern sensory projections by selectively repelling axons that normally terminate dorsally. Involved in the development of the olfactory system and in neuronal control of puberty (By similarity).By similarity

GO - Molecular functioni

  • chemorepellent activity Source: MGI
  • neuropilin binding Source: BHF-UCL
  • semaphorin receptor binding Source: MGI

GO - Biological processi

  • apoptotic process Source: Ensembl
  • axonal fasciculation Source: MGI
  • axon extension involved in axon guidance Source: BHF-UCL
  • axon guidance Source: MGI
  • axonogenesis involved in innervation Source: BHF-UCL
  • branchiomotor neuron axon guidance Source: ParkinsonsUK-UCL
  • dendrite morphogenesis Source: MGI
  • dichotomous subdivision of terminal units involved in salivary gland branching Source: MGI
  • facial nerve structural organization Source: ParkinsonsUK-UCL
  • facioacoustic ganglion development Source: ParkinsonsUK-UCL
  • gonadotrophin-releasing hormone neuronal migration to the hypothalamus Source: BHF-UCL
  • motor neuron axon guidance Source: ParkinsonsUK-UCL
  • negative chemotaxis Source: MGI
  • negative regulation of axon extension Source: MGI
  • negative regulation of axon extension involved in axon guidance Source: MGI
  • negative regulation of epithelial cell migration Source: MGI
  • nerve development Source: BHF-UCL
  • neural crest cell migration involved in autonomic nervous system development Source: ParkinsonsUK-UCL
  • neural crest cell migration involved in sympathetic nervous system development Source: BHF-UCL
  • neuron migration Source: BHF-UCL
  • olfactory bulb development Source: UniProtKB
  • positive regulation of male gonad development Source: BHF-UCL
  • positive regulation of neuron migration Source: BHF-UCL
  • regulation of axon extension involved in axon guidance Source: UniProtKB
  • regulation of heart rate Source: MGI
  • semaphorin-plexin signaling pathway Source: MGI
  • semaphorin-plexin signaling pathway involved in axon guidance Source: ParkinsonsUK-UCL
  • semaphorin-plexin signaling pathway involved in neuron projection guidance Source: BHF-UCL
  • sympathetic ganglion development Source: BHF-UCL
  • sympathetic neuron projection extension Source: BHF-UCL
  • sympathetic neuron projection guidance Source: BHF-UCL
  • trigeminal ganglion development Source: ParkinsonsUK-UCL
  • trigeminal nerve structural organization Source: ParkinsonsUK-UCL
  • ventral trunk neural crest cell migration Source: ParkinsonsUK-UCL
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis

Enzyme and pathway databases

ReactomeiR-MMU-399954. Sema3A PAK dependent Axon repulsion.
R-MMU-399955. SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion.
R-MMU-399956. CRMPs in Sema3A signaling.

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-3A
Alternative name(s):
Semaphorin III
Short name:
Sema III
Semaphorin-D
Short name:
Sema D
Gene namesi
Name:Sema3a
Synonyms:Semad, SemD
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:107558. Sema3a.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2020Sequence analysisAdd
BLAST
Chaini21 – 772752Semaphorin-3APRO_0000032304Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi53 – 531N-linked (GlcNAc...)1 Publication
Disulfide bondi103 ↔ 1141 Publication
Glycosylationi125 – 1251N-linked (GlcNAc...)1 Publication
Disulfide bondi132 ↔ 1411 Publication
Disulfide bondi269 ↔ 3811 Publication
Disulfide bondi293 ↔ 3411 Publication
Disulfide bondi517 ↔ 535By similarity
Glycosylationi591 – 5911N-linked (GlcNAc...)Sequence analysis
Disulfide bondi650 ↔ 723By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiO08665.
PaxDbiO08665.
PRIDEiO08665.

PTM databases

PhosphoSiteiO08665.

Expressioni

Developmental stagei

Expressed early in embryonic development (E11) in distinct regions of the neuroectoderm and mesoderm. Expression became more extensive at later stages.

Gene expression databases

BgeeiO08665.
ExpressionAtlasiO08665. baseline and differential.
GenevisibleiO08665. MM.

Interactioni

Subunit structurei

Interacts with PXND1.1 Publication

GO - Molecular functioni

  • neuropilin binding Source: BHF-UCL
  • semaphorin receptor binding Source: MGI

Protein-protein interaction databases

BioGridi203161. 2 interactions.
DIPiDIP-59997N.
IntActiO08665. 1 interaction.
STRINGi10090.ENSMUSP00000030714.

Structurei

Secondary structure

1
772
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi31 – 344Combined sources
Helixi36 – 405Combined sources
Turni41 – 433Combined sources
Beta strandi46 – 483Combined sources
Beta strandi59 – 635Combined sources
Turni64 – 674Combined sources
Beta strandi68 – 747Combined sources
Beta strandi76 – 838Combined sources
Beta strandi87 – 926Combined sources
Helixi97 – 1059Combined sources
Turni110 – 1134Combined sources
Beta strandi117 – 1237Combined sources
Beta strandi125 – 1339Combined sources
Beta strandi136 – 1383Combined sources
Beta strandi140 – 1456Combined sources
Beta strandi148 – 1514Combined sources
Beta strandi156 – 1649Combined sources
Turni166 – 1683Combined sources
Beta strandi171 – 1755Combined sources
Beta strandi178 – 1825Combined sources
Beta strandi185 – 1917Combined sources
Beta strandi199 – 20810Combined sources
Turni218 – 2203Combined sources
Beta strandi225 – 2328Combined sources
Beta strandi235 – 2373Combined sources
Helixi238 – 2403Combined sources
Beta strandi242 – 2509Combined sources
Beta strandi261 – 2699Combined sources
Beta strandi275 – 2806Combined sources
Beta strandi287 – 2915Combined sources
Beta strandi307 – 3148Combined sources
Beta strandi323 – 3297Combined sources
Beta strandi333 – 3353Combined sources
Beta strandi338 – 3436Combined sources
Helixi345 – 3528Combined sources
Beta strandi356 – 3583Combined sources
Beta strandi384 – 3874Combined sources
Helixi392 – 3943Combined sources
Helixi397 – 4048Combined sources
Beta strandi408 – 4114Combined sources
Helixi416 – 4183Combined sources
Beta strandi421 – 4299Combined sources
Beta strandi431 – 44010Combined sources
Beta strandi445 – 4539Combined sources
Beta strandi458 – 4625Combined sources
Beta strandi466 – 4683Combined sources
Beta strandi478 – 4803Combined sources
Beta strandi483 – 4853Combined sources
Beta strandi491 – 4955Combined sources
Turni496 – 4994Combined sources
Beta strandi500 – 5078Combined sources
Beta strandi509 – 5146Combined sources
Helixi517 – 5193Combined sources
Helixi524 – 5296Combined sources
Beta strandi539 – 5413Combined sources
Turni564 – 5663Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q47X-ray2.80A/B26-520[»]
4GZ8X-ray3.30A/B21-569[»]
4GZAX-ray7.00G21-555[»]
ProteinModelPortaliO08665.
SMRiO08665. Positions 26-664.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO08665.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 514484SemaPROSITE-ProRule annotationAdd
BLAST
Domaini579 – 66587Ig-like C2-typeAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi728 – 77043Arg/Lys-rich (basic)Add
BLAST

Domaini

Strong binding to neuropilin is mediated by the carboxy third of the protein.

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

Phylogenomic databases

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiO08665.
KOiK06840.
OMAiREPTTIS.
OrthoDBiEOG7VMP4F.
TreeFamiTF316102.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
SSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O08665-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGWFTGIACL FWGVLLTARA NYANGKNNVP RLKLSYKEML ESNNVITFNG
60 70 80 90 100
LANSSSYHTF LLDEERSRLY VGAKDHIFSF NLVNIKDFQK IVWPVSYTRR
110 120 130 140 150
DECKWAGKDI LKECANFIKV LEAYNQTHLY ACGTGAFHPI CTYIEVGHHP
160 170 180 190 200
EDNIFKLQDS HFENGRGKSP YDPKLLTASL LIDGELYSGT AADFMGRDFA
210 220 230 240 250
IFRTLGHHHP IRTEQHDSRW LNDPRFISAH LIPESDNPED DKVYFFFREN
260 270 280 290 300
AIDGEHSGKA THARIGQICK NDFGGHRSLV NKWTTFLKAR LICSVPGPNG
310 320 330 340 350
IDTHFDELQD VFLMNSKDPK NPIVYGVFTT SSNIFKGSAV CMYSMSDVRR
360 370 380 390 400
VFLGPYAHRD GPNYQWVPYQ GRVPYPRPGT CPSKTFGGFD STKDLPDDVI
410 420 430 440 450
TFARSHPAMY NPVFPINNRP IMIKTDVNYQ FTQIVVDRVD AEDGQYDVMF
460 470 480 490 500
IGTDVGTVLK VVSVPKETWH DLEEILLEEM TVFREPTTIS AMELSTKQQQ
510 520 530 540 550
LYIGSTAGVA QLPLHRCDIY GKACAECCLA RDPYCAWDGS SCSRYFPTAK
560 570 580 590 600
RRTRRQDIRN GDPLTHCSDL QHHDNHHGPS LEERIIYGVE NSSTFLECSP
610 620 630 640 650
KSQRALVYWQ FQRRNEDRKE EIRMGDHIIR TEQGLLLRSL QKKDSGNYLC
660 670 680 690 700
HAVEHGFMQT LLKVTLEVID TEHLEELLHK DDDGDGSKIK EMSSSMTPSQ
710 720 730 740 750
KVWYRDFMQL INHPNLNTMD EFCEQVWKRD RKQRRQRPGH SQGSSNKWKH
760 770
MQESKKGRNR RTHEFERAPR SV
Length:772
Mass (Da):88,813
Last modified:July 27, 2011 - v2
Checksum:iC6533FF007018D0C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti193 – 1931D → N in AAA73934 (PubMed:7748562).Curated
Sequence conflicti207 – 2071H → D in CAA59985 (PubMed:7748561).Curated
Sequence conflicti253 – 2531D → G in CAA59985 (PubMed:7748561).Curated
Sequence conflicti352 – 3521F → L in AAA73934 (PubMed:7748562).Curated
Sequence conflicti403 – 4031A → G in CAA59985 (PubMed:7748561).Curated
Sequence conflicti475 – 4751I → V in CAA59985 (PubMed:7748561).Curated
Sequence conflicti475 – 4751I → V in BAA19773 (PubMed:9331345).Curated
Sequence conflicti475 – 4751I → V in AAL77611 (Ref. 3) Curated
Sequence conflicti475 – 4751I → V in AAH57588 (PubMed:15489334).Curated
Sequence conflicti475 – 4751I → V in AAH90844 (PubMed:15489334).Curated
Sequence conflicti475 – 4751I → V in AAA73934 (PubMed:7748562).Curated
Sequence conflicti571 – 5722QH → ED in CAA59985 (PubMed:7748561).Curated
Sequence conflicti616 – 6205EDRKE → RRSKR in CAA59985 (PubMed:7748561).Curated
Sequence conflicti623 – 6231R → K in AAA73934 (PubMed:7748562).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85993 mRNA. Translation: CAA59985.1.
D85028 mRNA. Translation: BAA19773.1.
L41541 mRNA. Translation: AAL77611.1.
AC022368 Genomic DNA. No translation available.
AC109165 Genomic DNA. No translation available.
AC121125 Genomic DNA. No translation available.
AC121841 Genomic DNA. No translation available.
AC159971 Genomic DNA. No translation available.
BC057588 mRNA. Translation: AAH57588.1.
BC090844 mRNA. Translation: AAH90844.1.
L40484 mRNA. Translation: AAA73934.1.
CCDSiCCDS19092.1.
PIRiI48747.
I58169.
RefSeqiNP_001230001.1. NM_001243072.1.
NP_001230002.1. NM_001243073.1.
NP_033178.2. NM_009152.4.
XP_006503620.1. XM_006503557.2.
XP_006503621.1. XM_006503558.2.
XP_006503622.1. XM_006503559.1.
XP_011238967.1. XM_011240665.1.
UniGeneiMm.372039.
Mm.483774.

Genome annotation databases

EnsembliENSMUST00000030714; ENSMUSP00000030714; ENSMUSG00000028883.
ENSMUST00000095012; ENSMUSP00000092621; ENSMUSG00000028883.
GeneIDi20346.
KEGGimmu:20346.
UCSCiuc008wmb.3. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85993 mRNA. Translation: CAA59985.1.
D85028 mRNA. Translation: BAA19773.1.
L41541 mRNA. Translation: AAL77611.1.
AC022368 Genomic DNA. No translation available.
AC109165 Genomic DNA. No translation available.
AC121125 Genomic DNA. No translation available.
AC121841 Genomic DNA. No translation available.
AC159971 Genomic DNA. No translation available.
BC057588 mRNA. Translation: AAH57588.1.
BC090844 mRNA. Translation: AAH90844.1.
L40484 mRNA. Translation: AAA73934.1.
CCDSiCCDS19092.1.
PIRiI48747.
I58169.
RefSeqiNP_001230001.1. NM_001243072.1.
NP_001230002.1. NM_001243073.1.
NP_033178.2. NM_009152.4.
XP_006503620.1. XM_006503557.2.
XP_006503621.1. XM_006503558.2.
XP_006503622.1. XM_006503559.1.
XP_011238967.1. XM_011240665.1.
UniGeneiMm.372039.
Mm.483774.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q47X-ray2.80A/B26-520[»]
4GZ8X-ray3.30A/B21-569[»]
4GZAX-ray7.00G21-555[»]
ProteinModelPortaliO08665.
SMRiO08665. Positions 26-664.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi203161. 2 interactions.
DIPiDIP-59997N.
IntActiO08665. 1 interaction.
STRINGi10090.ENSMUSP00000030714.

PTM databases

PhosphoSiteiO08665.

Proteomic databases

MaxQBiO08665.
PaxDbiO08665.
PRIDEiO08665.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000030714; ENSMUSP00000030714; ENSMUSG00000028883.
ENSMUST00000095012; ENSMUSP00000092621; ENSMUSG00000028883.
GeneIDi20346.
KEGGimmu:20346.
UCSCiuc008wmb.3. mouse.

Organism-specific databases

CTDi10371.
MGIiMGI:107558. Sema3a.

Phylogenomic databases

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000039964.
HOVERGENiHBG055071.
InParanoidiO08665.
KOiK06840.
OMAiREPTTIS.
OrthoDBiEOG7VMP4F.
TreeFamiTF316102.

Enzyme and pathway databases

ReactomeiR-MMU-399954. Sema3A PAK dependent Axon repulsion.
R-MMU-399955. SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion.
R-MMU-399956. CRMPs in Sema3A signaling.

Miscellaneous databases

EvolutionaryTraceiO08665.
NextBioi298185.
PROiO08665.
SOURCEiSearch...

Gene expression databases

BgeeiO08665.
ExpressionAtlasiO08665. baseline and differential.
GenevisibleiO08665. MM.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
SSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Murine semaphorin D/collapsin is a member of a diverse gene family and creates domains inhibitory for axonal extension."
    Pueschel A.W., Adams R.H., Betz H.
    Neuron 14:941-948(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: NMRI.
    Tissue: Embryo.
  2. "Disruption of semaphorin III/D gene causes severe abnormality in peripheral nerve projection."
    Taniguchi M., Yuasa S., Fujisawa H., Naruse I., Saga S., Mishina M., Yagi T.
    Neuron 19:519-530(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "cDNA sequence of mouse collapsin/semaphorin III."
    Kimura T., Fishman M.C.
    Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  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].
    Strain: C57BL/6J.
    Tissue: Brain.
  6. "Semaphorin III can function as a selective chemorepellent to pattern sensory projections in the spinal cord."
    Messersmith E.K., Leonardo E.D., Shatz C.J., Tessier-Lavigne M., Goodman C.S., Kolodkin A.L.
    Neuron 14:949-959(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 107-772.
    Tissue: Fetal brain.
  7. "PlexinD1 and semaphorin signaling are required in endothelial cells for cardiovascular development."
    Gitler A.D., Lu M.M., Epstein J.A.
    Dev. Cell 7:107-116(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PLXND1.
  8. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 26-520, GLYCOSYLATION AT ASN-53 AND ASN-125, DISULFIDE BONDS.

Entry informationi

Entry nameiSEM3A_MOUSE
AccessioniPrimary (citable) accession number: O08665
Secondary accession number(s): E9QK85
, Q5BL08, Q62180, Q62215
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: May 11, 2016
This is version 145 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.