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Protein

Semaphorin-6A

Gene

Sema6a

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

Functioni

Cell surface receptor for PLXNA2 that plays an important role in cell-cell signaling. Required for normal granule cell migration in the developing cerebellum. Promotes reorganization of the actin cytoskeleton and plays an important role in axon guidance in the developing central nervous system. Can act as repulsive axon guidance cue. Has repulsive action towards migrating granular neurons. May play a role in channeling sympathetic axons into the sympathetic chains and controlling the temporal sequence of sympathetic target innervation.4 Publications

GO - Molecular functioni

  • chemorepellent activity Source: GO_Central
  • identical protein binding Source: IntAct
  • semaphorin receptor binding Source: MGI
  • transmembrane signaling receptor activity Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein
Biological processDifferentiation, Neurogenesis

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-6A
Alternative name(s):
Semaphorin Q
Short name:
Sema Q
Semaphorin VIA
Short name:
Sema VIA
Semaphorin-6A-1
Short name:
SEMA6A-1
Gene namesi
Name:Sema6a
Synonyms:Semaq
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 18

Organism-specific databases

MGIiMGI:1203727 Sema6a

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini19 – 649ExtracellularSequence analysisAdd BLAST631
Transmembranei650 – 670HelicalSequence analysisAdd BLAST21
Topological domaini671 – 1031CytoplasmicSequence analysisAdd BLAST361

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

No visible phenotype. Mice are viable and fertile, and do not show any major behavioral defects. In developing cerebellum, migration of granule cells is impaired. Granule cells can form normal cell processes, but the movement of the nucleus seems to be impaired.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi191L → R: Strongly reduced affinity for PLXNA2. 1 Publication1
Mutagenesisi212H → N: Strongly reduced affinity for PLXNA2. 1 Publication1
Mutagenesisi322I → E: Abolishes homodimerization. 1 Publication1
Mutagenesisi393K → E: Strongly reduced affinity for PLXNA2. 1 Publication1
Mutagenesisi415M → C: Formation of disulfide-linked homodimer. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 18Sequence analysisAdd BLAST18
ChainiPRO_000003234019 – 1031Semaphorin-6AAdd BLAST1013

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi33N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi49N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi65N-linked (GlcNAc...) asparagine1 Publication1
Disulfide bondi107 ↔ 117
Disulfide bondi135 ↔ 144
Disulfide bondi258 ↔ 369
Glycosylationi282N-linked (GlcNAc...) asparagine2 Publications1
Disulfide bondi283 ↔ 328
Glycosylationi434N-linked (GlcNAc...) asparagine2 Publications1
Glycosylationi461N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi477 ↔ 506
Disulfide bondi515 ↔ 533
Disulfide bondi521 ↔ 568
Disulfide bondi525 ↔ 542
Modified residuei698PhosphoserineBy similarity1
Modified residuei953PhosphoserineBy similarity1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

MaxQBiO35464
PaxDbiO35464
PRIDEiO35464

PTM databases

iPTMnetiO35464
PhosphoSitePlusiO35464

Expressioni

Tissue specificityi

Particularly high levels in spinal cord, cerebellum, metencephalon, superior and inferior colliculus, diencephalon, olfactory bulb and eye.1 Publication

Developmental stagei

Temporally and spatially regulated during development.

Gene expression databases

BgeeiENSMUSG00000019647 Expressed in 261 organ(s), highest expression level in cerebellum
ExpressionAtlasiO35464 baseline and differential
GenevisibleiO35464 MM

Interactioni

Subunit structurei

Active as a homodimer or oligomer. The SEMA6A homodimer interacts with a PLXNA2 homodimer, giving rise to a heterotetramer. Interacts with EVL.3 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

DIPiDIP-59220N
ELMiO35464
IntActiO35464, 2 interactors
MINTiO35464
STRINGi10090.ENSMUSP00000019791

Structurei

Secondary structure

11031
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO35464
SMRiO35464
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO35464

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini24 – 512SemaPROSITE-ProRule annotationAdd BLAST489

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi792 – 819Pro-richAdd BLAST28

Sequence similaritiesi

Belongs to the semaphorin family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3611 Eukaryota
ENOG410XQZC LUCA
GeneTreeiENSGT00760000119134
HOGENOMiHOG000232047
HOVERGENiHBG072910
InParanoidiO35464
KOiK06842
OMAiEYNSMGK
PhylomeDBiO35464
TreeFamiTF316102

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR002165 Plexin_repeat
IPR001627 Semap_dom
IPR036352 Semap_dom_sf
IPR027231 Semaphorin
IPR015943 WD40/YVTN_repeat-like_dom_sf
PANTHERiPTHR11036 PTHR11036, 1 hit
PfamiView protein in Pfam
PF01437 PSI, 1 hit
PF01403 Sema, 1 hit
SMARTiView protein in SMART
SM00630 Sema, 1 hit
SUPFAMiSSF101912 SSF101912, 1 hit
PROSITEiView protein in PROSITE
PS51004 SEMA, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 4 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: O35464-1) [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
MRPAALLLCL TLLHCAGAGF PEDSEPISIS HGNYTKQYPV FVGHKPGRNT
60 70 80 90 100
TQRHRLDIQM IMIMNRTLYV AARDHIYTVD IDTSHTEEIY CSKKLTWKSR
110 120 130 140 150
QADVDTCRMK GKHKDECHNF IKVLLKKNDD TLFVCGTNAF NPSCRNYRVD
160 170 180 190 200
TLETFGDEFS GMARCPYDAK HANIALFADG KLYSATVTDF LAIDAVIYRS
210 220 230 240 250
LGDSPTLRTV KHDSKWLKEP YFVQAVDYGD YIYFFFREIA VEYNTMGKVV
260 270 280 290 300
FPRVAQVCKN DMGGSQRVLE KQWTSFLKAR LNCSVPGDSH FYFNILQAVT
310 320 330 340 350
DVIRINGRDV VLATFSTPYN SIPGSAVCAY DMLDIANVFT GRFKEQKSPD
360 370 380 390 400
STWTPVPDER VPKPRPGCCA GSSSLEKYAT SNEFPDDTLN FIKTHPLMDE
410 420 430 440 450
AVPSIINRPW FLRTMVRYRL TKIAVDNAAG PYQNHTVVFL GSEKGIILKF
460 470 480 490 500
LARIGSSGFL NGSLFLEEMN VYNPEKCSYD GVEDKRIMGM QLDRASGSLY
510 520 530 540 550
VAFSTCVIKV PLGRCERHGK CKKTCIASRD PYCGWVRESG SCAHLSPLSR
560 570 580 590 600
LTFEQDIERG NTDGLGDCHN SFVALNGHAS SLYPSTTTSD SASRDGYESR
610 620 630 640 650
GGMLDWNDLL EAPGSTDPLG AVSSHNHQDK KGVIRESYLK SNDQLVPVTL
660 670 680 690 700
LAIAVILAFV MGAVFSGIIV YCVCDHRRKD VAVVQRKEKE LTHSRRGSMS
710 720 730 740 750
SVTKLSGLFG DTQSKDPKPE AILTPLMHNG KLATPSNTAK MLIKADQHHL
760 770 780 790 800
DLTALPTPES TPTLQQKRKP NRGSREWERN QNIINACTKD MPPMGSPVIP
810 820 830 840 850
TDLPLRASPS HIPSVVVLPI TQQGYQHEYV DQPKMSEVVA QMALEDQAAT
860 870 880 890 900
LEYKTIKEHL SSKSPNHGVN LVENLDSLPP KVPQREASLG PPGTSLSQTG
910 920 930 940 950
LSKRLEMQHS SSYGLEYKRS YPTNSLTRSH QTTTLKRNNT NSSNSSHLSR
960 970 980 990 1000
NQSFGRGDNP PPAPQRVDSI QVHSSQPSGQ AVTVSRQPSL NAYNSLTRSG
1010 1020 1030
LKRTPSLKPD VPPKPSFAPL STSMKPNDAC T
Length:1,031
Mass (Da):114,433
Last modified:December 7, 2004 - v2
Checksum:i38565A81A4DA3BDB
GO
Isoform 2 (identifier: O35464-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     439-464: Missing.

Show »
Length:1,005
Mass (Da):111,726
Checksum:i5C282E0436E9AA38
GO
Isoform 3 (identifier: O35464-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     577-631: Missing.

Note: No experimental confirmation available.
Show »
Length:976
Mass (Da):108,646
Checksum:i4EB77AD756326289
GO

Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D3YWM8D3YWM8_MOUSE
Semaphorin-6A
Sema6a
1,048Annotation score:
K3W4S5K3W4S5_MOUSE
Semaphorin-6A
Sema6a
1,005Annotation score:
D3YZJ8D3YZJ8_MOUSE
Semaphorin-6A
Sema6a
216Annotation score:
F6WLW8F6WLW8_MOUSE
Semaphorin-6A
Sema6a
111Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti172A → V in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti201L → P in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti337N → D in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti585S → N in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti685Q → R in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti703 – 704TK → SE in AAG29494 (PubMed:10993894).Curated2
Sequence conflicti735P → S in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti766Q → E in AAB86408 (PubMed:9204478).Curated1
Sequence conflicti856I → T in AAG29494 (PubMed:10993894).Curated1
Sequence conflicti863 – 888KSPNH…QREAS → ESSPYVLKQFSEAFNRQGII LSVAVE in AAB86408 (PubMed:9204478).CuratedAdd BLAST26

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_012097439 – 464Missing in isoform 2. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_012098577 – 631Missing in isoform 3. 1 PublicationAdd BLAST55

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF288666 mRNA Translation: AAG29494.1
BC059238 mRNA Translation: AAH59238.1
BC062979 mRNA Translation: AAH62979.1
AF030430 mRNA Translation: AAB86408.1
CCDSiCCDS37813.1 [O35464-1]
CCDS79642.1 [O35464-3]
RefSeqiNP_001298026.1, NM_001311097.1 [O35464-3]
NP_061214.2, NM_018744.2 [O35464-1]
UniGeneiMm.40909

Genome annotation databases

EnsembliENSMUST00000019791; ENSMUSP00000019791; ENSMUSG00000019647 [O35464-1]
ENSMUST00000076043; ENSMUSP00000075420; ENSMUSG00000019647 [O35464-3]
ENSMUST00000156422; ENSMUSP00000121442; ENSMUSG00000019647 [O35464-1]
GeneIDi20358
KEGGimmu:20358
UCSCiuc008ewa.1 mouse [O35464-1]
uc008ewb.1 mouse [O35464-3]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF288666 mRNA Translation: AAG29494.1
BC059238 mRNA Translation: AAH59238.1
BC062979 mRNA Translation: AAH62979.1
AF030430 mRNA Translation: AAB86408.1
CCDSiCCDS37813.1 [O35464-1]
CCDS79642.1 [O35464-3]
RefSeqiNP_001298026.1, NM_001311097.1 [O35464-3]
NP_061214.2, NM_018744.2 [O35464-1]
UniGeneiMm.40909

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3AFCX-ray2.50A/B19-570[»]
3AL8X-ray3.60A19-570[»]
3OKWX-ray2.30A/B19-571[»]
3OKYX-ray2.20B19-571[»]
ProteinModelPortaliO35464
SMRiO35464
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59220N
ELMiO35464
IntActiO35464, 2 interactors
MINTiO35464
STRINGi10090.ENSMUSP00000019791

PTM databases

iPTMnetiO35464
PhosphoSitePlusiO35464

Proteomic databases

MaxQBiO35464
PaxDbiO35464
PRIDEiO35464

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000019791; ENSMUSP00000019791; ENSMUSG00000019647 [O35464-1]
ENSMUST00000076043; ENSMUSP00000075420; ENSMUSG00000019647 [O35464-3]
ENSMUST00000156422; ENSMUSP00000121442; ENSMUSG00000019647 [O35464-1]
GeneIDi20358
KEGGimmu:20358
UCSCiuc008ewa.1 mouse [O35464-1]
uc008ewb.1 mouse [O35464-3]

Organism-specific databases

CTDi57556
MGIiMGI:1203727 Sema6a

Phylogenomic databases

eggNOGiKOG3611 Eukaryota
ENOG410XQZC LUCA
GeneTreeiENSGT00760000119134
HOGENOMiHOG000232047
HOVERGENiHBG072910
InParanoidiO35464
KOiK06842
OMAiEYNSMGK
PhylomeDBiO35464
TreeFamiTF316102

Miscellaneous databases

ChiTaRSiSema6a mouse
EvolutionaryTraceiO35464
PROiPR:O35464
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000019647 Expressed in 261 organ(s), highest expression level in cerebellum
ExpressionAtlasiO35464 baseline and differential
GenevisibleiO35464 MM

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR002165 Plexin_repeat
IPR001627 Semap_dom
IPR036352 Semap_dom_sf
IPR027231 Semaphorin
IPR015943 WD40/YVTN_repeat-like_dom_sf
PANTHERiPTHR11036 PTHR11036, 1 hit
PfamiView protein in Pfam
PF01437 PSI, 1 hit
PF01403 Sema, 1 hit
SMARTiView protein in SMART
SM00630 Sema, 1 hit
SUPFAMiSSF101912 SSF101912, 1 hit
PROSITEiView protein in PROSITE
PS51004 SEMA, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSEM6A_MOUSE
AccessioniPrimary (citable) accession number: O35464
Secondary accession number(s): Q6P5A8, Q6PCN9, Q9EQ71
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: December 7, 2004
Last modified: November 7, 2018
This is version 155 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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