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    SEMA6D semaphorin 6D [ Homo sapiens (human) ]

    Gene ID: 80031, updated on 10-Dec-2024

    Summary

    Official Symbol
    SEMA6Dprovided by HGNC
    Official Full Name
    semaphorin 6Dprovided by HGNC
    Primary source
    HGNC:HGNC:16770
    See related
    Ensembl:ENSG00000137872 MIM:609295; AllianceGenome:HGNC:16770
    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
    Summary
    Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
    Expression
    Broad expression in small intestine (RPKM 13.9), placenta (RPKM 10.4) and 19 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SEMA6D in Genome Data Viewer
    Location:
    15q21.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (47184089..47774228)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (44992008..45582270)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (47476286..48066425)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene cytochrome b5 type B-like Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:47425847-47426471 Neighboring gene uncharacterized LOC107984733 Neighboring gene RN7SK pseudogene 139 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:47697799-47698547 Neighboring gene uncharacterized LOC124900620 Neighboring gene uncharacterized LOC105370804 Neighboring gene Sharpr-MPRA regulatory region 212 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:48056535-48057734 Neighboring gene ribosomal protein L7a pseudogene 62 Neighboring gene LINC01491 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9371 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48143210-48144409 Neighboring gene long intergenic non-protein coding RNA 1491 Neighboring gene uncharacterized LOC124900354 Neighboring gene uncharacterized LOC102724553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9374

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome wide association study (GWAS) providing evidence of an association between common genetic variants and late radiotherapy toxicity.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Genome-wide association analysis of eating disorder-related symptoms, behaviors, and personality traits.
    EBI GWAS Catalog
    Novel genetic variants modify the effect of smoking on carotid plaque burden in Hispanics.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ11598, KIAA1479

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables receptor ligand activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in axon guidance 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 negative regulation of smooth muscle cell migration IEA
    Inferred from Electronic Annotation
    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 positive regulation of smooth muscle cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in semaphorin-plexin signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in smooth muscle cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventricular system development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    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
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

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

    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_029119.2 RefSeqGene

      Range
      538300..595023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001198999.2NP_001185928.1  semaphorin-6D isoform 1 precursor

      See identical proteins and their annotated locations for NP_001185928.1

      Status: REVIEWED

      Source sequence(s)
      AC066615, AF389427, BC150253
      Consensus CDS
      CCDS32224.1
      UniProtKB/TrEMBL
      A0A185QE25
      Related
      ENSP00000452815.1, ENST00000558014.5
      Conserved Domains (3) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl25496
      Location:8691005
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    2. NM_001358351.3NP_001345280.1  semaphorin-6D isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AC018900, AF389426, AK290032
      Consensus CDS
      CCDS32225.1
      UniProtKB/Swiss-Prot
      A6NF10, A6NM95, A6NNK1, A7E2A0, Q8NFY3, Q8NFY4, Q8NFY5, Q8NFY6, Q8NFY7, Q9P249
      UniProtKB/TrEMBL
      A8K1W7
      Related
      ENSP00000446152.3, ENST00000536845.7
      Conserved Domains (3) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514569
      PSI; Plexin repeat
      cl25496
      Location:9311067
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    3. NM_001358352.2NP_001345281.1  semaphorin-6D isoform 7 precursor

      Status: REVIEWED

      Source sequence(s)
      AC018900, AC044787, AF389428
      UniProtKB/TrEMBL
      A8K1W7
      Conserved Domains (3) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl25496
      Location:9441080
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    4. NM_020858.2NP_065909.1  semaphorin-6D isoform 1 precursor

      See identical proteins and their annotated locations for NP_065909.1

      Status: REVIEWED

      Source sequence(s)
      AC044787, AF389430
      Consensus CDS
      CCDS32224.1
      UniProtKB/TrEMBL
      A0A185QE25
      Related
      ENSP00000350770.4, ENST00000358066.8
      Conserved Domains (3) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514543
      PSI; Plexin repeat
      cl25496
      Location:8691005
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    5. NM_024966.3NP_079242.2  semaphorin-6D isoform 6 precursor

      See identical proteins and their annotated locations for NP_079242.2

      Status: REVIEWED

      Source sequence(s)
      AC018900, AC044787, AF389426
      Consensus CDS
      CCDS32229.1
      UniProtKB/Swiss-Prot
      Q8NFY4
      Related
      ENSP00000374076.3, ENST00000389425.7
      Conserved Domains (1) summary
      cl15693
      Location:49476
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    6. NM_153616.2NP_705869.1  semaphorin-6D isoform 2 precursor

      See identical proteins and their annotated locations for NP_705869.1

      Status: REVIEWED

      Source sequence(s)
      AC044787, AF389427
      Consensus CDS
      CCDS32227.1
      UniProtKB/TrEMBL
      A0A185QE25
      Related
      ENSP00000374079.3, ENST00000389428.7
      Conserved Domains (2) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514569
      PSI; Plexin repeat
    7. NM_153617.2NP_705870.1  semaphorin-6D isoform 3 precursor

      See identical proteins and their annotated locations for NP_705870.1

      Status: REVIEWED

      Source sequence(s)
      AC044787, AF389428
      Consensus CDS
      CCDS32226.1
      UniProtKB/TrEMBL
      A8K1W7
      Related
      ENSP00000346786.4, ENST00000354744.8
      Conserved Domains (2) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514569
      PSI; Plexin repeat
    8. NM_153618.2NP_705871.1  semaphorin-6D isoform 4 precursor

      See identical proteins and their annotated locations for NP_705871.1

      Status: REVIEWED

      Source sequence(s)
      AC044787, AF389429
      Consensus CDS
      CCDS32225.1
      UniProtKB/Swiss-Prot
      A6NF10, A6NM95, A6NNK1, A7E2A0, Q8NFY3, Q8NFY4, Q8NFY5, Q8NFY6, Q8NFY7, Q9P249
      UniProtKB/TrEMBL
      A8K1W7
      Related
      ENSP00000324857.5, ENST00000316364.9
      Conserved Domains (3) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514569
      PSI; Plexin repeat
      cl25496
      Location:9311067
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    9. NM_153619.1NP_705872.1  semaphorin-6D isoform 5 precursor

      See identical proteins and their annotated locations for NP_705872.1

      Status: REVIEWED

      Source sequence(s)
      AF389427, BC004330
      Consensus CDS
      CCDS32228.1
      UniProtKB/Swiss-Prot
      Q8NFY4
      Related
      ENSP00000348276.3, ENST00000355997.7
      Conserved Domains (2) summary
      cd11269
      Location:49513
      Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
      pfam01437
      Location:514569
      PSI; Plexin repeat

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      47184089..47774228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      44992008..45582270
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)