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SEMA3D semaphorin 3D [ Homo sapiens (human) ]

Gene ID: 223117, updated on 2-Nov-2024

Summary

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Official Symbol
SEMA3Dprovided by HGNC
Official Full Name
semaphorin 3Dprovided by HGNC
Primary source
HGNC:HGNC:10726
See related
Ensembl:ENSG00000153993 MIM:609907; AllianceGenome:HGNC:10726
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
coll-2; Sema-Z2
Summary
This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
Expression
Biased expression in spleen (RPKM 23.4), thyroid (RPKM 18.9) and 13 other tissues See more
Orthologs
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Genomic context

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See SEMA3D in Genome Data Viewer
Location:
7q21.11
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (84995553..85250243, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (86245383..86500064, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (84624869..84879559, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 11 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:84628763-84629962 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 8 Neighboring gene Sharpr-MPRA regulatory region 13705 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18338 Neighboring gene dynein light chain LC8-type 1 pseudogene 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:85053215-85054073 Neighboring gene long intergenic non-protein coding RNA 972

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Semaphorin 3D inhibits proliferation and migration of papillary thyroid carcinoma by regulating MAPK/ERK signaling pathway. Hai R, et al. Mol Biol Rep, 2022 May. PMID 35190928
  2. Semaphorin profiling of periodontal fibroblasts and osteoblasts. Lallier TE. J Dent Res, 2004 Sep. PMID 15329371
  3. Possible association of the semaphorin 3D gene (SEMA3D) with schizophrenia. Fujii T, et al. J Psychiatr Res, 2011 Jan. PMID 20684831
  4. Decreased expression of semaphorin 3D is associated with genesis and development in colorectal cancer. Wang Z, et al. World J Surg Oncol, 2017 Mar 20. PMID 28320475, Free PMC Article
  5. Tumor-derived semaphorin 3D promoting cancer cachexia via regulating hypothalamic pro-opiomelanocortin neurons. Zhang Y, et al. FASEB J, 2023 Jun. PMID 37219490

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Semaphorin 3D inhibits proliferation and migration of papillary thyroid carcinoma by regulating MAPK/ERK signaling pathway.
    Title: Semaphorin 3D inhibits proliferation and migration of papillary thyroid carcinoma by regulating MAPK/ERK signaling pathway.
  4. SEMA3D mRNA is expressed mainly in the cytoplasm of the endometrial cancer cells.
    Title: Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis.
  5. Low SEMA3D expression is associated with colorectal cancer.
    Title: Decreased expression of semaphorin 3D is associated with genesis and development in colorectal cancer.
  6. Novel mutation in SEMA3D segregates with the complete phenotype with variable expressivity in two pedigrees with autosomal dominant familial Meniere's disease.
    Title: Variable expressivity and genetic heterogeneity involving DPT and SEMA3D genes in autosomal dominant familial Meniere's disease.
  7. Data show significant increases in semaphorin3C, 3D and their receptor neuropilin-2 in degenerate samples which were shown to contain nerves and blood vessels, compared to non-degenerate samples without nerves and blood vessels.
    Title: Class 3 semaphorins expression and association with innervation and angiogenesis within the degenerate human intervertebral disc.
  8. CTNNA3 and SEMA3D: Promising loci for asthma exacerbation identified through multiple genome-wide association studies
    Title: CTNNA3 and SEMA3D: Promising loci for asthma exacerbation identified through multiple genome-wide association studies.
  9. Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability.
    Title: Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC39708

Gene Ontology Provided by GOA

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
  
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 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
collapsin 2
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (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.

Genomic

  1. NG_051329.2 RefSeqGene

    Range
    68187..259690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001384900.1 → NP_001371829.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Consensus CDS
    CCDS34676.1
    UniProtKB/Swiss-Prot
    A6NK46, O95025, Q6UW77, Q8NCQ1
    Related
    ENSP00000284136.6, ENST00000284136.11
    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

  2. NM_001384901.1 → NP_001371830.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Consensus CDS
    CCDS34676.1
    UniProtKB/Swiss-Prot
    A6NK46, O95025, Q6UW77, Q8NCQ1
    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

  3. NM_001384902.1 → NP_001371831.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Consensus CDS
    CCDS34676.1
    UniProtKB/Swiss-Prot
    A6NK46, O95025, Q6UW77, Q8NCQ1
    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

  4. NM_001384903.1 → NP_001371832.1  semaphorin-3D precursor

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Consensus CDS
    CCDS34676.1
    UniProtKB/Swiss-Prot
    A6NK46, O95025, Q6UW77, Q8NCQ1
    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

  5. NM_152754.3 → NP_689967.2  semaphorin-3D precursor

    See identical proteins and their annotated locations for NP_689967.2

    Status: REVIEWED

    Source sequence(s)
    AC004957, AC006151
    Consensus CDS
    CCDS34676.1
    UniProtKB/Swiss-Prot
    A6NK46, O95025, Q6UW77, Q8NCQ1
    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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    84995553..85250243 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420049.1 → XP_047276005.1  semaphorin-3D isoform X1

  2. XM_011515961.3 → XP_011514263.1  semaphorin-3D isoform X1

    Conserved Domains (4) summary
    cd05871
    Location:402 → 492
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    smart00410
    Location:417 → 486
    IG_like; Immunoglobulin like
    smart00423
    Location:339 → 376
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:1 → 340
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    86245383..86500064 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357611.1 → XP_054213586.1  semaphorin-3D isoform X1

  2. XM_054357610.1 → XP_054213585.1  semaphorin-3D isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95025.2 GenPept UniProtKB/Swiss-Prot:O95025

Gene LinkOut

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