Sema5a semaphorin 5A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema5aprovided by RGD
Official Full Name: semaphorin 5Aprovided by RGD
Primary source: RGD:1308650
See related: Ensembl:ENSRNOG00000011977 AllianceGenome:RGD:1308650
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: Enables chondroitin sulfate proteoglycan binding activity; heparan sulfate proteoglycan binding activity; and syndecan binding activity. Involved in nervous system development and signal clustering. Located in membrane. Orthologous to human SEMA5A (semaphorin 5A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 139.5), Uterus (RPKM 136.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q23

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (85020724..85451938)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (83309843..83741084)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (85377318..85808970)

Chromosome 2 - NC_086020.1 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
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?

Semaphorin5A expression in the developing chick telencephalon.
Title: Semaphorin5A expression in the developing chick telencephalon.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2Rat328 (e-PCR), detects polymorphism
- UniSTS:227462

UniSTS:496014 (e-PCR)
- UniSTS:496014

Sema5a (e-PCR), detects polymorphism
- UniSTS:496014

RH141406 (e-PCR)
- UniSTS:223401

Sema5a (e-PCR), detects polymorphism
- UniSTS:545981

D2MGH19 (e-PCR)
- UniSTS:121593

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables axon guidance receptor activity	ISO Inferred from Sequence Orthology more info
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables chondroitin sulfate proteoglycan binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables heparan sulfate proteoglycan binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IEA Inferred from Electronic Annotation more info
enables semaphorin receptor binding	ISO Inferred from Sequence Orthology more info
enables semaphorin receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables syndecan binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in axon extension	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon extension	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axonal fasciculation	IDA Inferred from Direct Assay more info	PubMed
involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within branching involved in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within branching morphogenesis of an epithelial tube	ISO Inferred from Sequence Orthology more info
involved_in cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in cell chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within detection of light stimulus involved in visual perception	ISO Inferred from Sequence Orthology more info
involved_in diencephalon development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of axon extension involved in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endothelial cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron projection extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection guidance	ISO Inferred from Sequence Orthology more info
involved_in positive chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of actin filament depolymerization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of actin filament depolymerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of axon extension involved in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of endothelial cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISS Inferred from Sequence or Structural Similarity 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
involved_in semaphorin-plexin signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal clustering	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in signal clustering	ISO Inferred from Sequence Orthology more info
involved_in signal clustering	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: semaphorin-5A

Names: sema F; sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A; semaphorin-F

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_001107659.2 → NP_001101129.1 semaphorin-5A precursor

See identical proteins and their annotated locations for NP_001101129.1

Status: VALIDATED

Source sequence(s)

AABR07009051, AABR07009052

UniProtKB/Swiss-Prot

D3ZTD8

Related

ENSRNOP00000016506.4, ENSRNOT00000016506.6

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat

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

85020724..85451938

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063281754.1 → XP_063137824.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

D3ZTD8
XM_063281755.1 → XP_063137825.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

D3ZTD8