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    SEMA6C semaphorin 6C [ Homo sapiens (human) ]

    Gene ID: 10500, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SEMA6Cprovided by HGNC
    Official Full Name
    semaphorin 6Cprovided by HGNC
    Primary source
    HGNC:HGNC:10740
    See related
    Ensembl:ENSG00000143434 MIM:609294; AllianceGenome:HGNC:10740
    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
    SEMAY; Sema-Y; m-SemaY; m-SemaY2
    Summary
    This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]
    Expression
    Broad expression in testis (RPKM 9.5), heart (RPKM 5.4) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEMA6C in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151131685..151146631, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150255406..150272108, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151104183..151119107, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene GA binding protein transcription factor subunit beta 2 Neighboring gene ribosomal protein S29 pseudogene 29 Neighboring gene uncharacterized LOC124904418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151104130-151104914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1315 Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene sodium channel modifier 1 Neighboring gene tropomodulin 4

    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. Emerging roles for semaphorins in neural regeneration. Pasterkamp RJ, et al. Brain Res Brain Res Rev, 2001 Mar. PMID 11245885
    2. Cloning and characterization of a novel class VI semaphorin, semaphorin Y. Kikuchi K, et al. Mol Cell Neurosci, 1999 Jan. PMID 10049528
    3. Identification, characterization, and functional study of the two novel human members of the semaphorin gene family. Qu X, et al. J Biol Chem, 2002 Sep 20. PMID 12110693
    4. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. Gregório SP, et al. Psychiatry Res, 2009 Jan 30. PMID 19054571
    5. Redifferentiation of dedifferentiated chondrocytes and chondrogenesis of human bone marrow stromal cells via chondrosphere formation with expression profiling by large-scale cDNA analysis. Imabayashi H, et al. Exp Cell Res, 2003 Aug 1. PMID 12878157

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence.
    2. identification, characterization, and functional study of the two novel human members of the semaphorin gene family
      Title: Identification, characterization, and functional study of the two novel human members of the semaphorin gene family.
    Submit: New GeneRIF Correction

    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

    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 negative regulation of axon extension IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 cell surface IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-6C
    Names
    sema Y
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C
    semaphorin-Y

    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_029237.1 RefSeqGene

      Range
      5034..19958
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001178061.3 → NP_001171532.1  semaphorin-6C isoform 1 precursor

      See identical proteins and their annotated locations for NP_001171532.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB022434, AF339154, AL592424, DA787858
      Consensus CDS
      CCDS53364.1
      UniProtKB/Swiss-Prot
      Q9H3T2
      Related
      ENSP00000357909.3, ENST00000368913.7
      Conserved Domains (2) summary
      pfam01437
      Location:518 → 570
      PSI; Plexin repeat
      cl15693
      Location:53 → 517
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. NM_001178062.3 → NP_001171533.1  semaphorin-6C isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      AB022434, AF339152, AF339153, AL592424, DA787858
      Consensus CDS
      CCDS53363.1
      UniProtKB/Swiss-Prot
      Q9H3T2
      Related
      ENSP00000357908.3, ENST00000368912.7
      Conserved Domains (2) summary
      pfam01437
      Location:478 → 530
      PSI; Plexin repeat
      cl15693
      Location:53 → 477
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. NM_030913.6 → NP_112175.2  semaphorin-6C isoform 2 precursor

      See identical proteins and their annotated locations for NP_112175.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      AB022434, AF339152, AL592424, DA787858
      Consensus CDS
      CCDS984.1
      UniProtKB/Swiss-Prot
      D3DV15, Q5JR71, Q5JR72, Q5JR73, Q8WXT8, Q8WXT9, Q8WXU0, Q96JF8, Q9H3T2
      Related
      ENSP00000357910.3, ENST00000368914.8
      Conserved Domains (2) summary
      pfam01437
      Location:518 → 570
      PSI; Plexin repeat
      cl15693
      Location:53 → 517
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      151131685..151146631 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431998.1 → XP_047287954.1  semaphorin-6C isoform X6

    2. XM_005244835.4 → XP_005244892.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_005244892.1

      UniProtKB/Swiss-Prot
      Q9H3T2
      Conserved Domains (2) summary
      pfam01437
      Location:518 → 570
      PSI; Plexin repeat
      cl15693
      Location:53 → 517
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_047431842.1 → XP_047287798.1  semaphorin-6C isoform X1

    4. XM_047431776.1 → XP_047287732.1  semaphorin-6C isoform X1

    5. XM_047431793.1 → XP_047287749.1  semaphorin-6C isoform X1

    6. XM_047431979.1 → XP_047287935.1  semaphorin-6C isoform X5

    7. XM_047431878.1 → XP_047287834.1  semaphorin-6C isoform X2

    8. XM_047431937.1 → XP_047287893.1  semaphorin-6C isoform X4

    9. XM_047431923.1 → XP_047287879.1  semaphorin-6C isoform X3

      UniProtKB/Swiss-Prot
      D3DV15, Q5JR71, Q5JR72, Q5JR73, Q8WXT8, Q8WXT9, Q8WXU0, Q96JF8, Q9H3T2

    10. XM_047432028.1 → XP_047287984.1  semaphorin-6C isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      150255406..150272108 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333868.1 → XP_054189843.1  semaphorin-6C isoform X1

    2. XM_054333869.1 → XP_054189844.1  semaphorin-6C isoform X2

    3. XM_054333866.1 → XP_054189841.1  semaphorin-6C isoform X1

    4. XM_054333867.1 → XP_054189842.1  semaphorin-6C isoform X1

    5. XM_054333872.1 → XP_054189847.1  semaphorin-6C isoform X5

    6. XM_054333871.1 → XP_054189846.1  semaphorin-6C isoform X4

    7. XM_054333870.1 → XP_054189845.1  semaphorin-6C isoform X3

    8. XM_054333874.1 → XP_054189849.1  semaphorin-6C isoform X7

    9. XM_054333873.1 → XP_054189848.1  semaphorin-6C isoform X6

      UniProtKB/TrEMBL
      B4DZD4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H3T2.4 GenPept UniProtKB/Swiss-Prot:Q9H3T2

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