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Aliases for SEMA3F Gene

Aliases for SEMA3F Gene

  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3F 2 3
  • Sema IV 2 3 4
  • Semaphorin IV 3 4
  • Sema III/F 3 4
  • SEMA4 3 6
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, 3F 3
  • Semaphorin III/F 3
  • Semaphorin-3F 3
  • SEMA-IV 3
  • SEMAK 3

External Ids for SEMA3F Gene

Summaries for SEMA3F Gene

Entrez Gene Summary for SEMA3F Gene

  • The semaphorins are a family of proteins that are involved in signaling. All the family members have a secretion signal, a 500-amino acid sema domain, and 16 conserved cysteine residues (Kolodkin et al., 1993 [PubMed 8269517]). Sequence comparisons have grouped the secreted semaphorins into 3 general classes, all of which also have an immunoglobulin domain. The semaphorin III family, consisting of human semaphorin III (SEMA3A; MIM 603961), chicken collapsin, and mouse semaphorins A, D, and E, all have a basic domain at the C terminus. Chicken collapsin contributes to path finding by axons during development by inhibiting extension of growth cones (Luo et al., 1993 [PubMed 8402908]) through an interaction with a collapsin response mediator protein of relative molecular mass 62K (CRMP62) (Goshima et al., 1995 [PubMed 7637782]), a putative homolog of an axonal guidance associated UNC33 gene product (MIM 601168). SEMA3F is a secreted member of the semaphorin III family.[supplied by OMIM, Mar 2008]

GeneCards Summary for SEMA3F Gene

SEMA3F (Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3F) is a Protein Coding gene. Diseases associated with SEMA3F include brachial plexus lesion and wallerian degeneration. Among its related pathways are Axon guidance. GO annotations related to this gene include receptor activity and chemorepellent activity. An important paralog of this gene is SEMA4G.

UniProtKB/Swiss-Prot for SEMA3F Gene

  • May play a role in cell motility and cell adhesion

Gene Wiki entry for SEMA3F Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA3F Gene

Genomics for SEMA3F Gene

Genomic Location for SEMA3F Gene

Start:
50,155,045 bp from pter
End:
50,189,075 bp from pter
Size:
34,031 bases
Orientation:
Plus strand

Genomic View for SEMA3F Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SEMA3F Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3F Gene

Regulatory Elements for SEMA3F Gene

Transcription factor binding sites by QIAGEN in the SEMA3F gene promoter:

Proteins for SEMA3F Gene

  • Protein details for SEMA3F Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13275-SEM3F_HUMAN
    Recommended name:
    Semaphorin-3F
    Protein Accession:
    Q13275
    Secondary Accessions:
    • C9JQ85
    • Q13274
    • Q13372
    • Q15704
    • Q6GTR4

    Protein attributes for SEMA3F Gene

    Size:
    785 amino acids
    Molecular mass:
    88381 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SEMA3F Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA3F Gene

Proteomics data for SEMA3F Gene at MOPED

Post-translational modifications for SEMA3F Gene

  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn53 and Asn126

Other Protein References for SEMA3F Gene

No data available for DME Specific Peptides for SEMA3F Gene

Domains for SEMA3F Gene

Gene Families for SEMA3F Gene

HGNC:
  • IGD :Immunoglobulin superfamily / Immunoglobulin-like domain containing
  • SEMA :Semaphorins

Suggested Antigen Peptide Sequences for SEMA3F Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13275

UniProtKB/Swiss-Prot:

SEM3F_HUMAN
Domain:
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.:
    • Q13275
  • Contains 1 Sema domain.:
    • Q13275
Family:
  • Belongs to the semaphorin family.:
    • Q13275
genes like me logo Genes that share domains with SEMA3F: view

Function for SEMA3F Gene

Molecular function for SEMA3F Gene

GENATLAS Biochemistry: semaphorin 3F,secreted,expressed in mammary gland,kidney,fetal brain,lung,repellent of the nerve growth cone guidance
UniProtKB/Swiss-Prot Function: May play a role in cell motility and cell adhesion

Gene Ontology (GO) - Molecular Function for SEMA3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IEA --
GO:0005515 protein binding --
GO:0045499 chemorepellent activity IDA 15814794
genes like me logo Genes that share ontologies with SEMA3F: view

Phenotypes for SEMA3F Gene

MGI mutant phenotypes for SEMA3F:
inferred from 4 alleles
GenomeRNAi human phenotypes for SEMA3F:
genes like me logo Genes that share phenotypes with SEMA3F: view

Animal Models for SEMA3F Gene

MGI Knock Outs for SEMA3F:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for SEMA3F Gene

Localization for SEMA3F Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3F Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SEMA3F Gene COMPARTMENTS Subcellular localization image for SEMA3F gene
Compartment Confidence
extracellular 4
plasma membrane 2
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SEMA3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space TAS 8786119
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SEMA3F: view

Pathways for SEMA3F Gene

SuperPathways for SEMA3F Gene

Superpath Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA3F: view

Pathways by source for SEMA3F Gene

1 KEGG pathway for SEMA3F Gene

Gene Ontology (GO) - Biological Process for SEMA3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration --
GO:0007275 multicellular organismal development --
GO:0007411 axon guidance IDA 15814794
GO:0021612 facial nerve structural organization IEA --
GO:0021637 trigeminal nerve structural organization IEA --
genes like me logo Genes that share ontologies with SEMA3F: view

Compounds for SEMA3F Gene

(1) Novoseek inferred chemical compound relationships for SEMA3F Gene

Compound -log(P) Hits PubMed IDs
vegf 64.6 17
genes like me logo Genes that share compounds with SEMA3F: view

Transcripts for SEMA3F Gene

Unigene Clusters for SEMA3F Gene

Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3F Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: - - - - -
SP3: - -
SP4: - - -
SP5: - -
SP6:

Relevant External Links for SEMA3F Gene

GeneLoc Exon Structure for
SEMA3F
ECgene alternative splicing isoforms for
SEMA3F

Expression for SEMA3F Gene

mRNA expression in normal human tissues for SEMA3F Gene

mRNA differential expression in normal tissues according to GTEx for SEMA3F Gene

This gene is overexpressed in Esophagus - Mucosa (5.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SEMA3F Gene

SOURCE GeneReport for Unigene cluster for SEMA3F Gene Hs.32981

mRNA Expression by UniProt/SwissProt for SEMA3F Gene

Q13275-SEM3F_HUMAN
Tissue specificity: Expressed abundantly but differentially in a variety of neural and nonneural tissues. There is high expression in mammary gland, kidney, fetal brain, and lung and lower expression in heart and liver
genes like me logo Genes that share expressions with SEMA3F: view

Orthologs for SEMA3F Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA3F Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA3F 35
  • 98.77 (n)
  • 98.47 (a)
SEMA3F 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA3F 35
  • 88.87 (n)
  • 93.12 (a)
SEMA3F 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA3F 35
  • 90.96 (n)
  • 96.94 (a)
SEMA3F 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema3f 35
  • 88.95 (n)
  • 96.42 (a)
Sema3f 16
Sema3f 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA3F 36
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA3F 36
  • 78 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema3f 35
  • 89.04 (n)
  • 95.8 (a)
chicken
(Gallus gallus)
Aves SEMA3F 35
  • 78.27 (n)
  • 82.33 (a)
SEMA3F 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA3F 36
  • 76 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC68870 35
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3f 35
  • 73.54 (n)
  • 81.11 (a)
zebrafish
(Danio rerio)
Actinopterygii sema3fa 36
  • 68 (a)
OneToMany
sema3fb 35
  • 67.4 (n)
  • 70.96 (a)
sema3fb 36
  • 69 (a)
OneToMany
sema3ga 36
  • 60 (a)
OneToMany
sema3gb 36
  • 61 (a)
OneToMany
Species with no ortholog for SEMA3F:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SEMA3F Gene

ENSEMBL:
Gene Tree for SEMA3F (if available)
TreeFam:
Gene Tree for SEMA3F (if available)

Paralogs for SEMA3F Gene

genes like me logo Genes that share paralogs with SEMA3F: view

Variants for SEMA3F Gene

Sequence variations from dbSNP and Humsavar for SEMA3F Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs14321 -- 50,188,718(+) CAGCC(C/T)CTTCA utr-variant-3-prime
rs756646 -- 50,158,819(-) CCCCA(C/T)AGCCC intron-variant
rs1046953 -- 50,159,664(+) CTGAC(C/T)GGGGC reference, synonymous-codon
rs1046955 - 50,184,779(+) TGCAG(C/G)CGACG reference, missense
rs1046956 - 50,185,493(+) AGGAG(A/T)TGGAG missense, reference, downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for SEMA3F Gene

Variant ID Type Subtype PubMed ID
nsv834690 CNV Loss 17160897
nsv515986 CNV Loss 19592680
nsv876768 CNV Gain 21882294
nsv523662 CNV Loss 19592680
nsv876769 CNV Loss 21882294
nsv470561 CNV Loss 18288195
nsv876770 CNV Loss 21882294
nsv523560 CNV Loss 19592680
dgv602n27 CNV Loss 19166990
dgv1456e1 CNV Complex 17122850
nsv834692 CNV Loss 17160897
nsv876771 CNV Loss 21882294

Relevant External Links for SEMA3F Gene

HapMap Linkage Disequilibrium report
SEMA3F

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA3F Gene

Disorders for SEMA3F Gene

(1) University of Copenhagen DISEASES for SEMA3F Gene

(8) Novoseek inferred disease relationships for SEMA3F Gene

Disease -log(P) Hits PubMed IDs
small cell lung cancer 50.8 3
cancer lung 41.6 18
tumors 29.9 26
primary tumor 3.24 1
metastasis 1.11 4

Relevant External Links for SEMA3F

Genetic Association Database (GAD)
SEMA3F
Human Genome Epidemiology (HuGE) Navigator
SEMA3F
genes like me logo Genes that share disorders with SEMA3F: view

No data available for UniProtKB/Swiss-Prot for SEMA3F Gene

Publications for SEMA3F Gene

  1. Isolation of the human semaphorin III/F gene (SEMA3F) at chromosome 3p21, a region deleted in lung cancer. (PMID: 8786119) Xiang R.-H. … Naylor S.L. (Genomics 1996) 2 3 4 23
  2. Distinct 3p21.3 deletions in lung cancer and identification of a new human semaphorin. (PMID: 8649831) Roche J. … Drabkin H. (Oncogene 1996) 2 3 4
  3. Human semaphorins A(V) and IV reside in the 3p21.3 small cell lung cancer deletion region and demonstrate distinct expression patterns. (PMID: 8633026) Sekido Y. … Minna J.D. (Proc. Natl. Acad. Sci. U.S.A. 1996) 3 4 23
  4. Semaphorin 3B and 3F single nucleotide polymorphisms are associated with prostate cancer risk and poor prognosis. (PMID: 19683737) Beuten J. … Naylor S.L. (J. Urol. 2009) 3 48
  5. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M. … Yamada Y. (Am. J. Hypertens. 2010) 3 48

Products for SEMA3F Gene

Sources for SEMA3F Gene

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