Sema4a semaphorin 4A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema4aprovided by RGD
Official Full Name: semaphorin 4Aprovided by RGD
Primary source: RGD:1304636
See related: EnsemblRapid:ENSRNOG00000019737 AllianceGenome:RGD:1304636
Gene type: protein coding
RefSeq status: VALIDATED
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. Predicted to be involved in several processes, including T-helper 1 cell differentiation; positive regulation of synapse assembly; and regulation of cell migration. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in cone-rod dystrophy 10 and retinitis pigmentosa 35. Orthologous to human SEMA4A (semaphorin 4A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 102.1), Lung (RPKM 88.2) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2q34

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (176194248..176215752, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (173896432..173917903, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (187799568..187823014, complement)

Chromosome 2 - NC_086020.1 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: 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

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 T cell differentiation involved in immune response	ISO Inferred from Sequence Orthology more info
involved_in T-helper 1 cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
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 positive regulation of excitatory synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of inhibitory synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of plasma membrane bounded cell projection organization	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: semaphorin-4A

Names: sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A

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_001012078.2 → NP_001012078.2 semaphorin-4A precursor

See identical proteins and their annotated locations for NP_001012078.2

Status: VALIDATED

Source sequence(s)

BC081943, JAXUCZ010000002

UniProtKB/TrEMBL

A0A1B0GWV9, A6J676, F7F3I7

Related

ENSRNOP00000053704.3, ENSRNOT00000056862.6

Conserved Domains (3) summary

smart00423
Location:498 → 542

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:567 → 639

Ig; Immunoglobulin domain

cl15693
Location:57 → 497

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

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_086020.1 Reference GRCr8

Range

176194248..176215752 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006232639.5 → XP_006232701.1 semaphorin-4A isoform X1

See identical proteins and their annotated locations for XP_006232701.1

UniProtKB/TrEMBL

A0A1B0GWV9, A6J676, F7F3I7

Conserved Domains (3) summary

smart00423
Location:498 → 542

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:567 → 639

Ig; Immunoglobulin domain

cl15693
Location:57 → 497

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_063281836.1 → XP_063137906.1 semaphorin-4A isoform X1

UniProtKB/TrEMBL

A6J676, F7F3I7
XM_063281837.1 → XP_063137907.1 semaphorin-4A isoform X1

UniProtKB/TrEMBL

A6J676, F7F3I7
XM_006232641.5 → XP_006232703.1 semaphorin-4A isoform X1

See identical proteins and their annotated locations for XP_006232703.1

UniProtKB/TrEMBL

A0A1B0GWV9, A6J676, F7F3I7

Conserved Domains (3) summary

smart00423
Location:498 → 542

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:567 → 639

Ig; Immunoglobulin domain

cl15693
Location:57 → 497

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_039102308.2 → XP_038958236.1 semaphorin-4A isoform X2

UniProtKB/TrEMBL

A0A1B0GWV9

Conserved Domains (4) summary

smart00423
Location:305 → 349

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:381 → 389

Ig; Ig strand B [structural motif]

cl11960
Location:379 → 446

Ig; Immunoglobulin domain

cl15693
Location:1 → 304

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_039102309.2 → XP_038958237.1 semaphorin-4A isoform X2

UniProtKB/TrEMBL

A0A1B0GWV9

Conserved Domains (4) summary

smart00423
Location:305 → 349

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:381 → 389

Ig; Ig strand B [structural motif]

cl11960
Location:379 → 446

Ig; Immunoglobulin domain

cl15693
Location:1 → 304

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