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    SEMA3D semaphorin 3D [ Homo sapiens (human) ]

    Gene ID: 223117, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Semaphorin 3D promotes pancreatic ductal adenocarcinoma progression and metastasis through macrophage reprogramming. Thielman NRJ, et al. Sci Adv, 2024 Oct 18. PMID 39413197

    See all (28) 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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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