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SEMA3F semaphorin 3F [ Homo sapiens (human) ]

Gene ID: 6405, updated on 7-Dec-2018

Summary

Official Symbol
SEMA3Fprovided by HGNC
Official Full Name
semaphorin 3Fprovided by HGNC
Primary source
HGNC:HGNC:10728
See related
Ensembl:ENSG00000001617 MIM:601124
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SEMA4; SEMAK; SEMA-IV
Summary
This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
Expression
Broad expression in skin (RPKM 21.7), esophagus (RPKM 16.4) and 19 other tissues See more
Orthologs

Genomic context

See SEMA3F in Genome Data Viewer
Location:
3p21.31
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (50155045..50189075)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50192562..50226508)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 6 Neighboring gene RBM5 antisense RNA 1 Neighboring gene RNA binding motif protein 5 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene basic proline-rich protein-like Neighboring gene G protein subunit alpha transducin 1 Neighboring gene solute carrier family 38 member 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from KEGG)
    Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, conserved biosystem (from KEGG)
    Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
branchiomotor neuron axon guidance IEA
Inferred from Electronic Annotation
more info
 
facial nerve structural organization IEA
Inferred from Electronic Annotation
more info
 
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nerve development ISS
Inferred from Sequence or Structural Similarity
more info
 
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neural crest cell migration involved in autonomic nervous system development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of postsynapse organization IEA
Inferred from Electronic Annotation
more info
 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin-plexin signaling pathway involved in axon guidance IEA
Inferred from Electronic Annotation
more info
 
semaphorin-plexin signaling pathway involved in neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
sympathetic ganglion development ISS
Inferred from Sequence or Structural Similarity
more info
 
sympathetic neuron projection extension ISS
Inferred from Sequence or Structural Similarity
more info
 
sympathetic neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
trigeminal nerve structural organization IEA
Inferred from Electronic Annotation
more info
 
ventral trunk neural crest cell migration IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
semaphorin-3F
Names
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3F
semaphorin III/F
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_001318798.1NP_001305727.1  semaphorin-3F isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the 5' coding region and initiates translation at a downstream start site, compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
    Source sequence(s)
    AB209259, AC000063, AC104450, BQ949723, CB240860
    Consensus CDS
    CCDS82780.1
    UniProtKB/TrEMBL
    C9JPG5, Q59G50
    Related
    ENSP00000388931.1, ENST00000413852.5
    Conserved Domains (4) summary
    cd05871
    Location:510598
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:1449
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:513597
    IG_like; Immunoglobulin like
    smart00423
    Location:448485
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. NM_001318800.1NP_001305729.1  semaphorin-3F isoform 2 precursor

    Status: REVIEWED

    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)
    AB209259, AC000063, AC104450, CB240860, U38276
    Consensus CDS
    CCDS82779.1
    UniProtKB/Swiss-Prot
    Q13275
    UniProtKB/TrEMBL
    Q59G50
    Related
    ENSP00000409859.1, ENST00000434342.5
    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. NM_004186.5NP_004177.3  semaphorin-3F isoform 1 precursor

    See identical proteins and their annotated locations for NP_004177.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AA378582, AC104450, BC042914, BF058597, CB240860
    Consensus CDS
    CCDS2811.1
    UniProtKB/Swiss-Prot
    Q13275
    Related
    ENSP00000002829.3, ENST00000002829.7
    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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    50155045..50189075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533998.2XP_011532300.1  semaphorin-3F isoform X1

    See identical proteins and their annotated locations for XP_011532300.1

    UniProtKB/Swiss-Prot
    Q13275
    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_005265382.4XP_005265439.1  semaphorin-3F isoform X2

    See identical proteins and their annotated locations for XP_005265439.1

    UniProtKB/Swiss-Prot
    Q13275
    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_011534000.2XP_011532302.1  semaphorin-3F isoform X4

    Conserved Domains (1) summary
    cl15693
    Location:48485
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. XM_006713290.3XP_006713353.1  semaphorin-3F isoform X5

    Conserved Domains (1) summary
    cl15693
    Location:48479
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. XM_005265381.4XP_005265438.1  semaphorin-3F isoform X1

    See identical proteins and their annotated locations for XP_005265438.1

    UniProtKB/Swiss-Prot
    Q13275
    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
  6. XM_006713289.3XP_006713352.1  semaphorin-3F isoform X3

    Conserved Domains (4) summary
    cd05871
    Location:412500
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    smart00410
    Location:415499
    IG_like; Immunoglobulin like
    smart00423
    Location:350387
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:17351
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RNA

  1. XR_940487.2 RNA Sequence

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