Sema3d sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema3dprovided by MGI
Official Full Name: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Dprovided by MGI
Primary source: MGI:MGI:1860118
See related: Ensembl:ENSMUSG00000040254 AllianceGenome:MGI:1860118
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 4631426B19Rik
Summary: Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including axon guidance; neural crest cell migration; and semaphorin-plexin signaling pathway. Located in extracellular space. Is expressed in several structures, including alimentary system; foot mesenchyme; intraembryonic coelom; nervous system; and sensory organ. Orthologous to human SEMA3D (semaphorin 3D). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in limb E14.5 (RPKM 4.3), bladder adult (RPKM 3.0) and 18 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 A1; 5 3.97 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (12433133..12638920)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (12383161..12588953)

Chromosome 5 - NC_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Semaphorin 3D promotes pancreatic ductal adenocarcinoma progression and metastasis through macrophage reprogramming.
Title: Semaphorin 3D promotes pancreatic ductal adenocarcinoma progression and metastasis through macrophage reprogramming.
Tumor-derived semaphorin 3D promoting cancer cachexia via regulating hypothalamic pro-opiomelanocortin neurons.
Title: Tumor-derived semaphorin 3D promoting cancer cachexia via regulating hypothalamic pro-opiomelanocortin neurons.
EGFR signaling is elevated in Sema3d (-/-) parathyroid glands and that pharmacological inhibition of EGFR signaling can partially rescue the parathyroid hyperplasia phenotype.
Title: Deficiency in the secreted protein Semaphorin3d causes abnormal parathyroid development in mice.
Semaphorin3D may contribute to enhanced bone loss by increased TNF-alpha in estrogen deficiency-induced osteoporosis.
Title: TNF-α promotes osteoclastogenesis through JNK signaling-dependent induction of Semaphorin3D expression in estrogen-deficiency induced osteoporosis.
Authors did not find evidence for genetic interaction between Ret and Sema3d affecting survival, presence of myenteric plexus or intestine transcriptome.
Title: Testing the Ret and Sema3d genetic interaction in mouse enteric nervous system development.
Data indicate that annexin A2 (AnxA2) regulates the secretion of semaphorin 3D (Sema3D) from pancreatic ductal adenocarcinoma (PDA) cells.
Title: Semaphorin 3D autocrine signaling mediates the metastatic role of annexin A2 in pancreatic cancer.
Semaphorin 3d requires neuropilin 1 or PI3K/Akt, whereas semaphorin 3e requires plexin D1 in directing endothelial motility.
Title: Semaphorin 3d and semaphorin 3e direct endothelial motility through distinct molecular signaling pathways.
In the absence of Sema3d, endothelial tubes form in a region that is normally avascular
Title: Semaphorin 3d signaling defects are associated with anomalous pulmonary venous connections.
Two proepicardial markers (Scleraxis and Semaphorin3D) were identified that genetically delineate heretofore uncharacterized proepicardial subcompartments.
Title: Distinct compartments of the proepicardial organ give rise to coronary vascular endothelial cells.
Sema 3D and Sema 3F genes are overlappingly and distinctly expressed in the developing parathyroid and thymus, respectively, and they might play roles in the interactions between these organs and surrounding tissues
Title: Expression of the semaphorins Sema 3D and Sema 3F in the developing parathyroid and thymus.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Sema3d (e-PCR), detects polymorphism
- UniSTS:166292

Gene Ontology Provided by MGI

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
enables semaphorin receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in nervous system development	IEA Inferred from Electronic Annotation 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 semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in extracellular space	HDA more info	PubMed
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

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_028882.4 → NP_083158.3 semaphorin-3D precursor

See identical proteins and their annotated locations for NP_083158.3

Status: VALIDATED

Source sequence(s)

AK052671, AK163828, CF746948

Consensus CDS

CCDS39013.1

UniProtKB/Swiss-Prot

Q8BH34

UniProtKB/TrEMBL

Q8BMF6

Related

ENSMUSP00000030868.7, ENSMUST00000030868.11

Conserved Domains (3) summary

cd05871
Location:596 → 686

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

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

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000071.7 Reference GRCm39 C57BL/6J

Range

12433133..12638920

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030254046.2 → XP_030109906.1 semaphorin-3D isoform X1

UniProtKB/Swiss-Prot

Q8BH34

UniProtKB/TrEMBL

Q8BMF6

Conserved Domains (3) summary

cd05871
Location:596 → 686

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

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