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Sema6c semaphorin 6C [ Rattus norvegicus (Norway rat) ]

Gene ID: 29744, updated on 11-Apr-2024

Summary

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Official Symbol
Sema6cprovided by RGD
Official Full Name
semaphorin 6Cprovided by RGD
Primary source
RGD:3659
See related
Ensembl:ENSRNOG00000021101 AllianceGenome:RGD:3659
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Involved in axon guidance. Predicted to be located in cell surface and cytoplasm. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA6C (semaphorin 6C). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Muscle (RPKM 75.7), Testes (RPKM 20.7) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Sema6c in Genome Data Viewer
Location:
2q34
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (185422636..185436237)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (182733635..182750066)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (196330777..196347218)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene sodium channel modifier 1 Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene uncharacterized LOC120100877 Neighboring gene GA binding protein transcription factor subunit beta 2 Neighboring gene MLLT11, transcription factor 7 cofactor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Cloning and characterization of a novel class VI semaphorin, semaphorin Y. Kikuchi K, et al. Mol Cell Neurosci, 1999 Jan. PMID 10049528
  2. 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
  3. PlexinA1 signaling directs the segregation of proprioceptive sensory axons in the developing spinal cord. Yoshida Y, et al. Neuron, 2006 Dec 7. PMID 17145500, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

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
  
enables semaphorin receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables semaphorin receptor binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axon guidance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of axon extension ISO
Inferred from Sequence Orthology
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
located_in cell surface ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
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-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.

mRNA and Protein(s)

  1. NM_017308.1 → NP_059004.1  semaphorin-6C precursor

    See identical proteins and their annotated locations for NP_059004.1

    Status: PROVISIONAL

    Source sequence(s)
    AB000817
    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Related
    ENSRNOP00000050221.1, ENSRNOT00000050914.4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    185422636..185436237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017590804.3 → XP_017446293.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  2. XM_017590800.3 → XP_017446289.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  3. XM_039102126.2 → XP_038958054.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  4. XM_006232858.5 → XP_006232920.1  semaphorin-6C isoform X1

    See identical proteins and their annotated locations for XP_006232920.1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  5. XM_063281681.1 → XP_063137751.1  semaphorin-6C isoform X2

    UniProtKB/TrEMBL
    A6K2W1

  6. XM_008761293.4 → XP_008759515.1  semaphorin-6C isoform X1

    See identical proteins and their annotated locations for XP_008759515.1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  7. XM_006232861.5 → XP_006232923.1  semaphorin-6C isoform X1

    See identical proteins and their annotated locations for XP_006232923.1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  8. XM_017590802.3 → XP_017446291.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  9. XM_017590806.3 → XP_017446295.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  10. XM_017590807.3 → XP_017446296.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  11. XM_017590809.3 → XP_017446298.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  12. XM_039102128.2 → XP_038958056.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  13. XM_017590808.3 → XP_017446297.1  semaphorin-6C isoform X1

    UniProtKB/Swiss-Prot
    Q9WTL3, Q9WTM6
    UniProtKB/TrEMBL
    A6K2V3, A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (3) summary
    PHA03307
    Location:730 → 956
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam01437
    Location:517 → 538
    PSI; Plexin repeat
    cl15693
    Location:52 → 516
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  14. XM_006232869.5 → XP_006232931.1  semaphorin-6C isoform X3

    UniProtKB/TrEMBL
    A6K2W3, A6K2W4, Q8R4U4
    Conserved Domains (2) summary
    pfam01437
    Location:472 → 493
    PSI; Plexin repeat
    cl15693
    Location:32 → 471
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9WTL3.1 GenPept UniProtKB/Swiss-Prot:Q9WTL3

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