SEMA4F ssemaphorin 4F [Homo sapiens (human)] - Gene

Summary

Official Symbol: SEMA4Fprovided by HGNC
Official Full Name: ssemaphorin 4Fprovided by HGNC
Primary source: HGNC:HGNC:10734
See related: Ensembl:ENSG00000135622 MIM:603706; AllianceGenome:HGNC:10734
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: S4F; SEMAM; SEMAW; M-SEMA; PRO2353; m-Sema-M
Summary: This gene encodes a transmembrane class IV semaphorin family protein, which plays a role in neural development. This gene may be involved in neurogenesis in prostate cancer, the development of neurofibromas, and breast cancer tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
Expression: Broad expression in brain (RPKM 2.1), testis (RPKM 1.1) and 22 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2p13.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (74654247..74709713)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (74662820..74718286)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (74881374..74910968)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

data seems to indicate that SEMA4F is involved in tumour progression in breast cancer
Title: Semaphorin-plexin signalling genes associated with human breast tumourigenesis.
Sema4F levels were strongly reduced in a panel of human neurofibromas, confirming the relevance of these findings to the human disease.
Title: NF1 loss disrupts Schwann cell-axonal interactions: a novel role for semaphorin 4F.
Fine mapping of the chromosome 2p12-16 dyslexia susceptibility candidate gene
Title: Fine mapping of the chromosome 2p12-16 dyslexia susceptibility locus: quantitative association analysis and positional candidate genes SEMA4F and OTX1.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic variants on chromosome 1q41 influence ocular axial length and high myopia. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D11S2921 (e-PCR)
- UniSTS:152074

PMC156606P1 (e-PCR)
- UniSTS:271408

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

WI-13990 (e-PCR)
- UniSTS:76614

L18426 (e-PCR)
- UniSTS:34648

D17S1239 (e-PCR)
- UniSTS:149852

Cda10e10 (e-PCR)
- UniSTS:45936

D2S2657 (e-PCR)
- UniSTS:54902

D11S3114 (e-PCR)
- UniSTS:152207

SEMA4F_810 (e-PCR)
- UniSTS:277701

STS-F02243 (e-PCR)
- UniSTS:81115

PMC26812P2 (e-PCR)
- UniSTS:272354

A008R45 (e-PCR)
- UniSTS:16101

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of axon extension	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinal ganglion cell axon guidance	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in perikaryon	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: semaphorin-4F

Names: sema domain immunoglobulin domain transmembrane domain (TM) and short cytoplasmic domain (semaphorin) 4F; sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F; semaphorin M; semaphorin-W

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

NM_001271661.2 → NP_001258590.1 semaphorin-4F isoform 2 precursor

See identical proteins and their annotated locations for NP_001258590.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks several internal exons, resulting in the loss of an in-frame segment in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AC007387, BC018361, CK905501, DC306380

Consensus CDS

CCDS62942.1

UniProtKB/Swiss-Prot

O95754

Related

ENSP00000342675.5, ENST00000339773.9

Conserved Domains (3) summary

pfam01437
Location:357 → 408

PSI; Plexin repeat

cl11960
Location:415 → 494

Ig; Immunoglobulin domain

cl15693
Location:52 → 356

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
NM_001271662.2 → NP_001258591.1 semaphorin-4F isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an internal in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.

Source sequence(s)

AC007387, AK308166, AL136552, CK905501, DC306380

Consensus CDS

CCDS74529.1

UniProtKB/TrEMBL

A0A087WYZ7

Related

ENSP00000407698.2, ENST00000434486.6

Conserved Domains (3) summary

cd11261
Location:52 → 478

Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)

pfam01437
Location:479 → 530

PSI; Plexin repeat

cl11960
Location:537 → 616

Ig; Immunoglobulin domain
NM_004263.5 → NP_004254.2 semaphorin-4F isoform 1 precursor

See identical proteins and their annotated locations for NP_004254.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC007387, AL136552, CK905501, DC306380

Consensus CDS

CCDS1955.1

UniProtKB/Swiss-Prot

O95754, Q542Y7, Q9NS35

Related

ENSP00000350547.2, ENST00000357877.7

Conserved Domains (3) summary

cd05872
Location:570 → 649

Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B

cd11261
Location:52 → 511

Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)

pfam01437
Location:512 → 563

PSI; Plexin repeat

RNA

NR_073398.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC007387, AK312728, CK905501, DC306380
NR_073399.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB021292, AC007387, AL136552, CK905501, DC306380

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

74654247..74709713

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047442927.1 → XP_047298883.1 semaphorin-4F isoform X6
XM_047442929.1 → XP_047298885.1 semaphorin-4F isoform X8
XM_047442926.1 → XP_047298882.1 semaphorin-4F isoform X2
XM_011532477.4 → XP_011530779.1 semaphorin-4F isoform X6

Conserved Domains (2) summary

cd11261
Location:52 → 511

Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)

pfam01437
Location:512 → 563

PSI; Plexin repeat
XM_011532476.4 → XP_011530778.1 semaphorin-4F isoform X5

Conserved Domains (2) summary

cd11261
Location:52 → 511

Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)

pfam01437
Location:512 → 563

PSI; Plexin repeat
XM_047442928.1 → XP_047298884.1 semaphorin-4F isoform X7
XM_011532475.4 → XP_011530777.1 semaphorin-4F isoform X4

Related

ENSP00000520881.1, ENST00000850594.1

Conserved Domains (3) summary

cd11261
Location:52 → 511

Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)

pfam01437
Location:512 → 563

PSI; Plexin repeat

cl11960
Location:570 → 616

Ig; Immunoglobulin domain
XM_017003172.2 → XP_016858661.1 semaphorin-4F isoform X1
XM_017003173.2 → XP_016858662.1 semaphorin-4F isoform X3