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    SEMA3D semaphorin 3D [ Homo sapiens (human) ]

    Gene ID: 223117, updated on 9-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    semaphorin-3D
    Names
    collapsin 2
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001384900.1NP_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:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:595686
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    2. NM_001384901.1NP_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:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:595686
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    3. NM_001384902.1NP_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:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:595686
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    4. NM_001384903.1NP_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:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:595686
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    5. NM_152754.3NP_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:61534
      Sema_3D; The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)
      smart00423
      Location:533570
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd05871
      Location:595686
      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_047420049.1XP_047276005.1  semaphorin-3D isoform X1

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

      Conserved Domains (4) summary
      cd05871
      Location:402492
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      smart00410
      Location:417486
      IG_like; Immunoglobulin like
      smart00423
      Location:339376
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl15693
      Location:1340
      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_054357611.1XP_054213586.1  semaphorin-3D isoform X1

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