Format

Send to:

Choose Destination

Sema3f sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [ Mus musculus (house mouse) ]

Gene ID: 20350, updated on 9-Sep-2018

Summary

Official Symbol
Sema3fprovided by MGI
Official Full Name
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fprovided by MGI
Primary source
MGI:MGI:1096347
See related
Ensembl:ENSMUSG00000034684 Vega:OTTMUSG00000050787
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Sema4; Semak
Expression
Broad expression in lung adult (RPKM 77.6), limb E14.5 (RPKM 39.8) and 19 other tissues See more
Orthologs

Genomic context

See Sema3f in Genome Data Viewer
Location:
9; 9 F1
Exon count:
21
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 9 NC_000075.6 (107681499..107710475, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (107583833..107612806, complement)

Chromosome 9 - NC_000075.6Genomic Context describing neighboring genes Neighboring gene solute carrier family 38, member 3 Neighboring gene guanine nucleotide binding protein, alpha transducing 1 Neighboring gene predicted gene, 34605 Neighboring gene RNA binding motif protein 5

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from BioSystems

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemorepellent activity IDA
Inferred from Direct Assay
more info
PubMed 
chemorepellent activity ISO
Inferred from Sequence Orthology
more info
PubMed 
neuropilin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
axon extension involved in axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
axon guidance ISO
Inferred from Sequence Orthology
more info
PubMed 
branchiomotor neuron axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
facial nerve structural organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
locomotion IC
Inferred by Curator
more info
PubMed 
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
negative chemotaxis IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of axon extension involved in axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of axon extension involved in axon guidance IGI
Inferred from Genetic Interaction
more info
PubMed 
nerve development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neural crest cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural crest cell migration involved in autonomic nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of postsynapse organization IDA
Inferred from Direct Assay
more info
PubMed 
regulation of postsynapse organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin-plexin signaling pathway involved in axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
semaphorin-plexin signaling pathway involved in neuron projection guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
sympathetic ganglion development IMP
Inferred from Mutant Phenotype
more info
PubMed 
sympathetic neuron projection extension IMP
Inferred from Mutant Phenotype
more info
PubMed 
sympathetic neuron projection guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
trigeminal nerve structural organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
ventral trunk neural crest cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
extracellular region IEA
Inferred from Electronic Annotation
more info
 
extracellular space HDA PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
semaphorin-3F
Names
semaphorin IV

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001311151.1NP_001298080.1  semaphorin-3F isoform 1 precursor

    See identical proteins and their annotated locations for NP_001298080.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK053632, CF736303, CX566341
    Consensus CDS
    CCDS81069.1
    UniProtKB/Swiss-Prot
    O88632
    Related
    ENSMUSP00000141865.1, OTTMUSP00000069357, ENSMUST00000192727.5, OTTMUST00000129015
    Conserved Domains (4) summary
    cd05871
    Location:609697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:612696
    IG_like; Immunoglobulin like
    smart00423
    Location:547584
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. NM_011349.3NP_035479.2  semaphorin-3F isoform 2 precursor

    See identical proteins and their annotated locations for NP_035479.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AK053632
    Consensus CDS
    CCDS23505.1
    UniProtKB/Swiss-Prot
    O88632
    Related
    ENSMUSP00000079400.3, OTTMUSP00000069225, ENSMUST00000080560.8, OTTMUST00000128718
    Conserved Domains (4) summary
    cd05871
    Location:578666
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:581665
    IG_like; Immunoglobulin like
    smart00423
    Location:516553
    PSI; domain found in Plexins, Semaphorins and Integrins

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000075.6 Reference GRCm38.p4 C57BL/6J

    Range
    107681499..107710475 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017313228.1XP_017168717.1  semaphorin-3F isoform X3

    UniProtKB/Swiss-Prot
    O88632
    Conserved Domains (4) summary
    cd05871
    Location:609697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:612696
    IG_like; Immunoglobulin like
    smart00423
    Location:547584
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. XM_006511676.3XP_006511739.1  semaphorin-3F isoform X4

    See identical proteins and their annotated locations for XP_006511739.1

    UniProtKB/Swiss-Prot
    O88632
    Conserved Domains (4) summary
    cd05871
    Location:578666
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:581665
    IG_like; Immunoglobulin like
    smart00423
    Location:516553
    PSI; domain found in Plexins, Semaphorins and Integrins
  3. XM_017313230.1XP_017168719.1  semaphorin-3F isoform X5

  4. XM_017313229.1XP_017168718.1  semaphorin-3F isoform X5

  5. XM_017313227.1XP_017168716.1  semaphorin-3F isoform X2

  6. XM_017313226.1XP_017168715.1  semaphorin-3F isoform X1

RNA

  1. XR_379758.3 RNA Sequence

  2. XR_871078.2 RNA Sequence

  3. XR_379759.3 RNA Sequence

Support Center