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SEMA6C semaphorin 6C [ Homo sapiens (human) ]

Gene ID: 10500, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151131685..151146631, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150255406..150272108, complement)
105.20220307 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
  • 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 (15) 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 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 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_2023_10

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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