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

Gene ID: 108151, updated on 18-Apr-2024

Summary

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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 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 act upstream of or within cell differentiation and nervous system development. Located in extracellular space. Is expressed in several structures, including alimentary system; foot mesenchyme; intraembryonic coelom; respiratory system; and sensory organ. Orthologous to human SEMA3D (semaphorin 3D). [provided by Alliance of Genome Resources, Apr 2022]
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

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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_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_12440 Neighboring gene predicted gene, 54301 Neighboring gene 2-cell-stage, variable group, member 3-like pseudogene Neighboring gene VISTA enhancer mm832 Neighboring gene predicted gene 8925 Neighboring gene STARR-seq mESC enhancer starr_12442 Neighboring gene STARR-seq mESC enhancer starr_12443 Neighboring gene predicted gene 42580 Neighboring gene STARR-seq mESC enhancer starr_12444 Neighboring gene STARR-seq mESC enhancer starr_12445 Neighboring gene STARR-seq mESC enhancer starr_12446 Neighboring gene STARR-seq mESC enhancer starr_12448 Neighboring gene STARR-seq mESC enhancer starr_12449 Neighboring gene STARR-seq mESC enhancer starr_12450 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Tumor-derived semaphorin 3D promoting cancer cachexia via regulating hypothalamic pro-opiomelanocortin neurons. Zhang Y, et al. FASEB J, 2023 Jun. PMID 37219490
  2. Testing the Ret and Sema3d genetic interaction in mouse enteric nervous system development. Kapoor A, et al. Hum Mol Genet, 2017 May 15. PMID 28334784, Free PMC Article
  3. TNF-α promotes osteoclastogenesis through JNK signaling-dependent induction of Semaphorin3D expression in estrogen-deficiency induced osteoporosis. Sang C, et al. J Cell Physiol, 2017 Dec. PMID 28059444
  4. Semaphorin 3D autocrine signaling mediates the metastatic role of annexin A2 in pancreatic cancer. Foley K, et al. Sci Signal, 2015 Aug 4. PMID 26243191, Free PMC Article
  5. Semaphorin 3d and semaphorin 3e direct endothelial motility through distinct molecular signaling pathways. Aghajanian H, et al. J Biol Chem, 2014 Jun 27. PMID 24825896, Free PMC Article

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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)
  • Targeted (5)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

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
  
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within 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 region IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular space HDA 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)

  1. 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

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    12433133..12638920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BH34.1 GenPept UniProtKB/Swiss-Prot:Q8BH34

Gene LinkOut

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