Sema3d semaphorin 3D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema3dprovided by RGD
Official Full Name: semaphorin 3Dprovided by RGD
Primary source: RGD:727939
See related: Ensembl:ENSRNOG00000007202 AllianceGenome:RGD:727939
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 and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA3D (semaphorin 3D). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 149.7), Kidney (RPKM 92.6) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q12

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (23271815..23460971, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (22316769..22505930, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (19224378..19413519, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Sema3D may regulate the axonal navigation of the large diameter DRG neurons.
Title: Expression of Sema3D in subsets of neurons in the developing dorsal root ganglia of the rat.
Gene regulation, via an alternative splicing mechanism, affects not only the tissue-specificity of Sema 3D expression, but also the distance over which it can act.
Title: Identification and tissue-specific expression of a novel isoform of Semaphorin 3D.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chemorepellent activity	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 negative chemotaxis	IBA Inferred from Biological aspect of Ancestor 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 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

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor 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-3D

Names: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D; semaphorin, homolog of the avian Sema3D

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_001104633.1 → NP_001098103.1 semaphorin-3D

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A7M6E9, F1MAG8

Related

ENSRNOP00000009489.5, ENSRNOT00000009489.7

Conserved Domains (3) summary

cd11252
Location:61 → 534

Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)

smart00423
Location:533 → 570

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:595 → 686

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3