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Protein

Semaphorin-6A

Gene

Sema6a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
  • semaphorin receptor binding Source: MGI
  • transmembrane signaling receptor activity Source: UniProtKB

GO - Biological processi

  • apoptotic process Source: UniProtKB
  • axon guidance Source: UniProtKB
  • cell surface receptor signaling pathway Source: MGI
  • centrosome localization Source: MGI
  • negative regulation of axon extension involved in axon guidance Source: GO_Central
  • neural crest cell migration Source: GO_Central
  • neuron migration Source: UniProtKB
  • positive regulation of neuron migration Source: UniProtKB
  • semaphorin-plexin signaling pathway Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis

Enzyme and pathway databases

ReactomeiR-MMU-416700. Other semaphorin interactions.

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 18

Organism-specific databases

MGIiMGI:1203727. Sema6a.

Subcellular locationi

Topology

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

GO - Cellular componenti

  • axon Source: UniProtKB
  • integral component of plasma membrane Source: UniProtKB
  • membrane Source: UniProtKB
  • plasma membrane Source: Reactome
Complete GO annotation...

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...)Sequence analysis1
Glycosylationi49N-linked (GlcNAc...)Sequence analysis1
Glycosylationi65N-linked (GlcNAc...)1 Publication1
Disulfide bondi107 ↔ 117
Disulfide bondi135 ↔ 144
Disulfide bondi258 ↔ 369
Glycosylationi282N-linked (GlcNAc...)2 Publications1
Disulfide bondi283 ↔ 328
Glycosylationi434N-linked (GlcNAc...)2 Publications1
Glycosylationi461N-linked (GlcNAc...)Sequence 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.
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

WithEntry#Exp.IntActNotes
Plxna4Q80UG23EBI-8057848,EBI-8057809

GO - Molecular functioni

  • semaphorin receptor binding Source: MGI

Protein-protein interaction databases

DIPiDIP-59220N.
IntActiO35464. 1 interactor.
MINTiMINT-7996710.
STRINGi10090.ENSMUSP00000019791.

Structurei

Secondary structure

11031
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi27 – 30Combined sources4
Helixi32 – 35Combined sources4
Beta strandi60 – 64Combined sources5
Beta strandi67 – 71Combined sources5
Beta strandi73 – 80Combined sources8
Helixi81 – 83Combined sources3
Beta strandi86 – 89Combined sources4
Beta strandi93 – 96Combined sources4
Helixi101 – 109Combined sources9
Turni114 – 116Combined sources3
Beta strandi120 – 128Combined sources9
Beta strandi131 – 136Combined sources6
Turni138 – 140Combined sources3
Beta strandi143 – 148Combined sources6
Turni149 – 151Combined sources3
Beta strandi154 – 160Combined sources7
Turni162 – 164Combined sources3
Beta strandi174 – 178Combined sources5
Beta strandi181 – 189Combined sources9
Beta strandi195 – 200Combined sources6
Turni214 – 216Combined sources3
Beta strandi221 – 228Combined sources8
Beta strandi231 – 239Combined sources9
Helixi241 – 243Combined sources3
Beta strandi244 – 247Combined sources4
Beta strandi250 – 258Combined sources9
Beta strandi266 – 269Combined sources4
Beta strandi277 – 281Combined sources5
Beta strandi287 – 289Combined sources3
Beta strandi295 – 299Combined sources5
Beta strandi303 – 305Combined sources3
Beta strandi308 – 316Combined sources9
Beta strandi319 – 322Combined sources4
Beta strandi325 – 331Combined sources7
Helixi332 – 338Combined sources7
Beta strandi343 – 348Combined sources6
Beta strandi353 – 355Combined sources3
Helixi358 – 360Combined sources3
Turni374 – 377Combined sources4
Helixi381 – 383Combined sources3
Helixi386 – 394Combined sources9
Beta strandi397 – 400Combined sources4
Helixi405 – 407Combined sources3
Beta strandi410 – 413Combined sources4
Beta strandi415 – 418Combined sources4
Beta strandi420 – 429Combined sources10
Turni430 – 433Combined sources4
Beta strandi435 – 442Combined sources8
Beta strandi445 – 452Combined sources8
Helixi455 – 457Combined sources3
Beta strandi464 – 470Combined sources7
Helixi474 – 477Combined sources4
Beta strandi489 – 493Combined sources5
Helixi494 – 496Combined sources3
Beta strandi498 – 502Combined sources5
Beta strandi507 – 512Combined sources6
Helixi516 – 518Combined sources3
Helixi522 – 527Combined sources6
Beta strandi533 – 536Combined sources4
Turni537 – 540Combined sources4
Beta strandi541 – 544Combined sources4
Beta strandi557 – 559Combined sources3

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...

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
Contains 1 Sema domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

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

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR002165. Plexin_repeat.
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]
SMARTiSM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
PROSITEiPS51004. SEMA. 1 hit.
[Graphical view]

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

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

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

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.
IntActiO35464. 1 interactor.
MINTiMINT-7996710.
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.
PhylomeDBiO35464.
TreeFamiTF316102.

Enzyme and pathway databases

ReactomeiR-MMU-416700. Other semaphorin interactions.

Miscellaneous databases

ChiTaRSiSema6a. mouse.
EvolutionaryTraceiO35464.
PROiO35464.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000019647.
ExpressionAtlasiO35464. baseline and differential.
GenevisibleiO35464. MM.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR002165. Plexin_repeat.
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]
SMARTiSM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
PROSITEiPS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSEM6A_MOUSE
AccessioniPrimary (citable) accession number: O35464
Secondary accession number(s): Q6P5A8, Q6PCN9, Q9EQ71
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: December 7, 2004
Last modified: November 30, 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.