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O88632 (SEM3F_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Semaphorin-3F
Alternative name(s):
Semaphorin IV
Short name=Sema IV
Gene names
Name:Sema3f
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length785 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Subcellular location

Secreted By similarity.

Tissue specificity

Expressed ubiquitously in adulthood. During embryogenesis, expressed in subregions of the central nervous system and various other tissues like skin, kidney, lung and intestine.

Sequence similarities

Belongs to the semaphorin family.

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

Contains 1 Sema domain.

Ontologies

Keywords
   Cellular componentSecreted
   Coding sequence diversityAlternative splicing
   DomainImmunoglobulin domain
Signal
   PTMDisulfide bond
Glycoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processaxon extension involved in axon guidance

Inferred from mutant phenotype PubMed 22790009. Source: BHF-UCL

axon guidance

Inferred from direct assay PubMed 12435358. Source: MGI

branchiomotor neuron axon guidance

Inferred from mutant phenotype PubMed 18804103. Source: ParkinsonsUK-UCL

facial nerve structural organization

Inferred from mutant phenotype PubMed 18804103. Source: ParkinsonsUK-UCL

negative chemotaxis

Inferred from direct assay PubMed 16319111. Source: MGI

negative regulation of axon extension involved in axon guidance

Inferred from direct assay PubMed 9753685. Source: MGI

nerve development

Inferred from mutant phenotype PubMed 22790009. Source: BHF-UCL

neural crest cell migration

Inferred from mutant phenotype PubMed 16319111. Source: MGI

semaphorin-plexin signaling pathway involved in axon guidance

Inferred from mutant phenotype PubMed 18804103. Source: ParkinsonsUK-UCL

semaphorin-plexin signaling pathway involved in neuron projection guidance

Inferred from mutant phenotype PubMed 22790009. Source: BHF-UCL

sympathetic ganglion development

Inferred from mutant phenotype PubMed 22790009. Source: BHF-UCL

sympathetic neuron projection extension

Inferred from mutant phenotype PubMed 22790009. Source: BHF-UCL

sympathetic neuron projection guidance

Inferred from mutant phenotype PubMed 22790009. Source: BHF-UCL

trigeminal nerve structural organization

Inferred from mutant phenotype PubMed 18804103. Source: ParkinsonsUK-UCL

   Cellular_componentextracellular region

Inferred from electronic annotation. Source: UniProtKB-SubCell

membrane

Inferred from electronic annotation. Source: InterPro

   Molecular_functionchemorepellent activity

Inferred from direct assay PubMed 11683995PubMed 12435358PubMed 16319111. Source: MGI

receptor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform B (identifier: O88632-1)

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 A (identifier: O88632-2)

The sequence of this isoform differs from the canonical sequence as follows:
     153-183: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1818 Potential
Chain19 – 785767Semaphorin-3F
PRO_0000032321

Regions

Domain31 – 545515Sema
Domain605 – 69591Ig-like C2-type
Compositional bias715 – 7184Poly-Pro
Compositional bias758 – 77922Arg/Lys-rich (basic)

Amino acid modifications

Glycosylation531N-linked (GlcNAc...) Potential
Glycosylation1261N-linked (GlcNAc...) Potential
Disulfide bond104 ↔ 115 By similarity
Disulfide bond133 ↔ 142 By similarity
Disulfide bond300 ↔ 412 By similarity
Disulfide bond324 ↔ 372 By similarity
Disulfide bond548 ↔ 566 By similarity
Disulfide bond678 ↔ 746 By similarity

Natural variations

Alternative sequence153 – 18331Missing in isoform A.
VSP_006042

Experimental info

Sequence conflict3501V → I in AAC28108. Ref.1
Sequence conflict3501V → I in AAC28109. Ref.1
Sequence conflict3501V → I in AAH10976. Ref.3
Sequence conflict7561R → S in AAC28108. Ref.1
Sequence conflict7561R → S in AAC28109. Ref.1
Sequence conflict7561R → S in AAH10976. Ref.3

Sequences

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

Last modified July 27, 2011. Version 2.
Checksum: 8F3F0935096C24A1

FASTA78588,549
        10         20         30         40         50         60 
MLVTAFILWA SLLTGAWPAT PIQDQLPATP RVRLSFKELK ATGTAHFFNF LLNTTDYRIL 

        70         80         90        100        110        120 
LKDEDHDRMY VGSKDYVLSL DLHDINREPL IIHWAASPQR IEECILSGKD GNGECGNFVR 

       130        140        150        160        170        180 
LIQPWNRTHL YVCGTGAYNP MCTYVNRGRR AQALPWTQMQ VVRGRGSRAT DGADRPTPTA 

       190        200        210        220        230        240 
PRQDYIFYLE PEKLESGKGK CPYDPKLDTA SALINEELYA GVYIDFMGTD AAIFRTLGKQ 

       250        260        270        280        290        300 
TAMRTDQYNS RWLNDPSFIH AELIPDSAER NDDKLYFFFR ERSAEAPQNP AVYARIGRIC 

       310        320        330        340        350        360 
LNDDGGHCCL VNKWSTFLKA RLVCSVPGED GIETHFDELQ DVFVQQTQDV RNPVIYAVFT 

       370        380        390        400        410        420 
SSGSVFRGSA VCVYSMADIR MVFNGPFAHK EGPNYQWMPF SGKMPYPRPG TCPGGTFTPS 

       430        440        450        460        470        480 
MKSTKDYPDE VINFMRTHPL MYQAVYPLQR RPLVVRTGAP YRLTTVAVDQ VDAADGRYEV 

       490        500        510        520        530        540 
LFLGTDRGTV QKVIVLPKDD QEVEELMLEE VEVFKEPAPV KTMTISSKRQ QLYVASAVGV 

       550        560        570        580        590        600 
THLSLHRCQA YGAACADCCL ARDPYCAWDG QACSRYTASS KRRSRRQDVR HGNPIRQCRG 

       610        620        630        640        650        660 
FNSNANKNAV ESVQYGVAGS AAFLECQPRS PQATVKWLFQ RDPSDRRREI RAEDRFLRTE 

       670        680        690        700        710        720 
QGLLLRALQL GDRGLYSCTA TENNFKHIVT RVQLHVLGRD AVHAALFPPL AVSVPPPPGT 

       730        740        750        760        770        780 
GPPTPPYQEL AQLLAQPEVG LIHQYCQGYW RHVPPRPREA PGALRPPELQ DQKKPRNRRH 


HPPDT 

« Hide

Isoform A [UniParc].

Checksum: 9A876D2AF2658EF3
Show »

FASTA75485,189

References

« Hide 'large scale' references
[1]"Cloning and expression pattern of a murine semaphorin homologous to H-sema IV."
Eckhardt F., Meyerhans A.
NeuroReport 9:3975-3979(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B).
[2]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C57BL/6J.
[3]"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 A).
Strain: FVB/N.
Tissue: Colon.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF080090 mRNA. Translation: AAC28108.1.
AF080091 mRNA. Translation: AAC28109.1.
AC152718 Genomic DNA. No translation available.
AC162905 Genomic DNA. No translation available.
BC010976 mRNA. Translation: AAH10976.1.
CCDSCCDS23505.1. [O88632-2]
RefSeqNP_035479.2. NM_011349.3. [O88632-2]
XP_006511738.1. XM_006511675.1. [O88632-1]
XP_006511739.1. XM_006511676.1. [O88632-2]
UniGeneMm.12903.

3D structure databases

ProteinModelPortalO88632.
SMRO88632. Positions 30-697.
ModBaseSearch...
MobiDBSearch...

PTM databases

PhosphoSiteO88632.

Proteomic databases

PaxDbO88632.
PRIDEO88632.

Protocols and materials databases

DNASU20350.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000080560; ENSMUSP00000079400; ENSMUSG00000034684. [O88632-2]
GeneID20350.
KEGGmmu:20350.
UCSCuc009rms.1. mouse. [O88632-1]
uc009rmt.1. mouse. [O88632-2]

Organism-specific databases

CTD6405.
MGIMGI:1096347. Sema3f.

Phylogenomic databases

eggNOGNOG320723.
GeneTreeENSGT00690000102148.
HOGENOMHOG000039964.
HOVERGENHBG055071.
InParanoidO88632.
KOK06840.
OMAACSRYTA.
OrthoDBEOG7034G7.
TreeFamTF352628.

Gene expression databases

BgeeO88632.
GenevestigatorO88632.

Family and domain databases

Gene3D2.130.10.10. 2 hits.
2.60.40.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003598. Ig_sub2.
IPR016201. Plexin-like_fold.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERPTHR11036. PTHR11036. 1 hit.
PfamPF01403. Sema. 1 hit.
[Graphical view]
SMARTSM00408. IGc2. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMSSF101912. SSF101912. 2 hits.
SSF103575. SSF103575. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSEMA3F. mouse.
NextBio298203.
PROO88632.
SOURCESearch...

Entry information

Entry nameSEM3F_MOUSE
AccessionPrimary (citable) accession number: O88632
Secondary accession number(s): E9QNC5, O88633
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: July 9, 2014
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot