Sema4f ssemaphorin 4F [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema4fprovided by RGD
Official Full Name: ssemaphorin 4Fprovided by RGD
Primary source: RGD:3658
See related: EnsemblRapid:ENSRNOG00000006784 AllianceGenome:RGD:3658
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in axon guidance. Acts upstream of or within negative regulation of axon extension and retinal ganglion cell axon guidance. Located in postsynaptic membrane. Is active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human SEMA4F (ssemaphorin 4F). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 36.9), Lung (RPKM 32.4) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (116969137..116995442, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (115411411..115437721, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (113738225..113764532, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

Sema4f (e-PCR), detects polymorphism
- UniSTS:144393

D4Wox51 (e-PCR)
- UniSTS:518686

D6UmiJ23 (e-PCR), detects polymorphism
- UniSTS:260416

Gene Ontology Provided by RGD

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 axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of axon extension	IDA Inferred from Direct Assay 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
acts_upstream_of_or_within retinal ganglion cell axon guidance	IDA Inferred from Direct Assay more info	PubMed
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	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IDA Inferred from Direct Assay 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 plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: semaphorin-4F

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

NCBI Reference Sequences (RefSeq)

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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_019272.2 → NP_062145.1 semaphorin-4F precursor

See identical proteins and their annotated locations for NP_062145.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q9Z143

UniProtKB/TrEMBL

A6IAI3

Related

ENSRNOP00000009269.4, ENSRNOT00000009269.6

Conserved Domains (3) summary

cd11261
Location:57 → 516

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

pfam01437
Location:517 → 568

PSI; Plexin repeat

cl11960
Location:575 → 654

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

116969137..116995442 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039107372.2 → XP_038963300.1 semaphorin-4F isoform X1

Conserved Domains (4) summary

pfam01437
Location:238 → 289

PSI; Plexin repeat

cd00096
Location:296 → 301

Ig; Ig strand A [structural motif]

cl11960
Location:296 → 375

Ig; Immunoglobulin domain

cl15693
Location:55 → 237

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins