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    Slitrk6 SLIT and NTRK-like family, member 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 290467, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Slitrk6provided by RGD
    Official Full Name
    SLIT and NTRK-like family, member 6provided by RGD
    Primary source
    RGD:1306550
    See related
    EnsemblRapid:ENSRNOG00000022337 AllianceGenome:RGD:1306550
    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 be involved in axonogenesis and positive regulation of synapse assembly. Predicted to act upstream of or within several processes, including auditory behavior; linear vestibuloocular reflex; and nervous system development. Predicted to be located in cell periphery and cell surface. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in high myopia-sensorineural deafness syndrome. Orthologous to human SLITRK6 (SLIT and NTRK like family member 6). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 58.6), Lung (RPKM 57.1) and 6 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Slitrk6 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (93977812..93984431, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (87563506..87570125, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (95507632..95514259, complement)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134482008 Neighboring gene heterogeneous nuclear ribonucleoprotein A1, pseudogene 27 Neighboring gene WD repeat domain 12, pseudogene 2 Neighboring gene eukaryotic translation initiation factor 4A2, pseudogene 1

    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 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. Impaired auditory-vestibular functions and behavioral abnormalities of Slitrk6-deficient mice. Matsumoto Y, et al. PLoS One, 2011 Jan 26. PMID 21298075, Free PMC Article
    2. SLITRK6 mutations cause myopia and deafness in humans and mice. Tekin M, et al. J Clin Invest, 2013 May. PMID 23543054, Free PMC Article
    3. Disorganized innervation and neuronal loss in the inner ear of Slitrk6-deficient mice. Katayama K, et al. PLoS One, 2009 Nov 11. PMID 19936227, Free PMC Article
    4. Identification and characterization of Slitrk, a novel neuronal transmembrane protein family controlling neurite outgrowth. Aruga J, et al. Mol Cell Neurosci, 2003 Sep. PMID 14550773
    5. Calsyntenins function as synaptogenic adhesion molecules in concert with neurexins. Um JW, et al. Cell Rep, 2014 Mar 27. PMID 24613359, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within auditory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within auditory receptor cell morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axonogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within camera-type eye development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cochlea development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within inner ear morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within innervation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lens development in camera-type eye ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within linear vestibuloocular reflex ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within multicellular organism growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron projection morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within startle response ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within vestibular reflex ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within vestibulocochlear nerve development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within visual perception ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cell periphery ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    SLIT and NTRK-like protein 6

    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_001106057.1 → NP_001099527.1  SLIT and NTRK-like protein 6 precursor

      See identical proteins and their annotated locations for NP_001099527.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473951
      UniProtKB/TrEMBL
      A6HUD3, D3ZP44
      Related
      ENSRNOP00000034471.4, ENSRNOT00000038433.6
      Conserved Domains (6) summary
      smart00082
      Location:516 → 566
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:210 → 222
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:94 → 113
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:388 → 425
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:387 → 444
      LRR_8; Leucine rich repeat
      cl15307
      Location:218 → 268
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    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_086033.1 Reference GRCr8

      Range
      93977812..93984431 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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