Sema4d semaphorin 4D [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Sema4dprovided by RGD
Full Name: semaphorin 4Dprovided by RGD
Primary source: RGD:1310554
See related: EnsemblRapid:ENSRNOG00000013679 AllianceGenome:RGD:1310554
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 identical protein binding activity; signaling receptor binding activity; and transmembrane signaling receptor activity. Predicted to be involved in several processes, including positive regulation of intracellular signal transduction; positive regulation of nervous system development; and regulation of peptidyl-tyrosine phosphorylation. Predicted to act upstream of or within positive regulation of axonogenesis. Is active in postsynaptic membrane. Orthologous to human SEMA4D (semaphorin 4D). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 145.3), Thymus (RPKM 118.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17p14

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (13582085..13688889)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (13430324..13537146)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (13516276..13538513)

Chromosome 17 - NC_086035.1 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?

[The role of semaphorin 4D in the mechanism of bisphosphonate-related osteonecrosis of the jaw in rats].
Title: [The role of semaphorin 4D in the mechanism of bisphosphonate-related osteonecrosis of the jaw in rats].
These results demonstrate a novel physiological function for sema4D/plxnB1 signaling in retinal pigment epithelium phagocytosis.
Title: Semaphorin4D-PlexinB1 Signaling Attenuates Photoreceptor Outer Segment Phagocytosis by Reducing Rac1 Activity of RPE Cells.
Skeletal fluorosis in vitro is caused by inhibition of osteogenesis via Sema4D/Plexin-B1 signaling pathway.
Title: Role of inhibition of osteogenesis function by Sema4D/Plexin-B1 signaling pathway in skeletal fluorosis in vitro.
sema4D knockdown in OPCs inhibited wound tissue angiogenesis and inflammation genes expression and upregulated axon regeneration genes expression at early phase
Title: Analysis of gene expression profiles associated with functional recovery after spinal cord injury caused by sema4D knockdown in oligodendrocytes.
role of Sema4D expression in spinal cord injury
Title: Sema4D knockdown in oligodendrocytes promotes functional recovery after spinal cord injury.
Sema4D regulates GABAergic synaptogenesis exclusively through its extracellular domain in rat hippocampus.
Title: Sema4D localizes to synapses and regulates GABAergic synapse development as a membrane-bound molecule in the mammalian hippocampus.
Sema4D/Plexin-B1 promotes the dephosphorylation and activation of PTEN through the R-Ras GAP activity, inducing growth cone collapse.
Title: Semaphorin 4D/Plexin-B1 stimulates PTEN activity through R-Ras GTPase-activating protein activity, inducing growth cone collapse in hippocampal neurons.

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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 identical protein binding	ISO Inferred from Sequence Orthology more info
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables receptor ligand activity	ISO Inferred from Sequence Orthology more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info
enables transmembrane signaling receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in bone trabecula morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in leukocyte aggregation	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 cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification involved in bone maturation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of GTPase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of Rho protein signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of collateral sprouting	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of inhibitory synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology 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 protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell projection organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of dendrite morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of synapse assembly	ISO Inferred from Sequence Orthology 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 GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	ISO Inferred from Sequence Orthology 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 membrane	IDA Inferred from Direct Assay more info	PubMed
part_of semaphorin receptor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: semaphorin-4D

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

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_001170563.2 → NP_001164034.1 semaphorin-4D precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000017

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

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_086035.1 Reference GRCr8

Range

13582085..13688889

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039095650.2 → XP_038951578.1 semaphorin-4D isoform X5

UniProtKB/TrEMBL

A0A096MJH1

Related

ENSRNOP00000068126.2, ENSRNOT00000076794.3

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
XM_039095647.2 → XP_038951575.1 semaphorin-4D isoform X2

UniProtKB/TrEMBL

A0A8I6GJZ1

Related

ENSRNOP00000091940.1, ENSRNOT00000106280.2

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_039095648.2 → XP_038951576.1 semaphorin-4D isoform X3

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_063276352.1 → XP_063132422.1 semaphorin-4D isoform X6

Related

ENSRNOP00000018378.9, ENSRNOT00000018378.10
XM_039095649.2 → XP_038951577.1 semaphorin-4D isoform X4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_063276349.1 → XP_063132419.1 semaphorin-4D isoform X4
XM_039095639.2 → XP_038951567.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_039095652.2 → XP_038951580.1 semaphorin-4D isoform X7

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_039095643.2 → XP_038951571.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_063276351.1 → XP_063132421.1 semaphorin-4D isoform X5

UniProtKB/TrEMBL

A0A096MJH1
XM_039095642.2 → XP_038951570.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_063276350.1 → XP_063132420.1 semaphorin-4D isoform X5

UniProtKB/TrEMBL

A0A096MJH1
XM_039095644.2 → XP_038951572.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Related

ENSRNOP00000079766.1, ENSRNOT00000101493.2

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_039095641.2 → XP_038951569.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_039095651.2 → XP_038951579.1 semaphorin-4D isoform X5

UniProtKB/TrEMBL

A0A096MJH1

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
XM_063276348.1 → XP_063132418.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4
XM_039095640.2 → XP_038951568.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_039095645.2 → XP_038951573.1 semaphorin-4D isoform X1

UniProtKB/TrEMBL

A0A8I6G5Q1, D3ZYR4

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain