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    Slitrk6 SLIT and NTRK-like family, member 6 [ Mus musculus (house mouse) ]

    Gene ID: 239250, updated on 28-Oct-2024

    Summary

    Official Symbol
    Slitrk6provided by MGI
    Official Full Name
    SLIT and NTRK-like family, member 6provided by MGI
    Primary source
    MGI:MGI:2443198
    See related
    Ensembl:ENSMUSG00000045871 AllianceGenome:MGI:2443198
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Sltk6; 4832410J21Rik
    Summary
    Acts upstream of or within several processes, including auditory behavior; linear vestibuloocular reflex; and nervous system development. Located in cell periphery. Is expressed in several structures, including brain; gut; limb bud; lung; and sensory organ. Used to study high myopia-sensorineural deafness syndrome and sensorineural hearing loss. 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, Oct 2024]
    Expression
    Biased expression in bladder adult (RPKM 3.5), limb E14.5 (RPKM 3.4) and 10 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Slitrk6 in Genome Data Viewer
    Location:
    14 E3; 14 57.2 cM
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (110984770..110992640, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (110747338..110755204, complement)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 25670 Neighboring gene predicted gene, 26255 Neighboring gene actin, beta pseudogene Neighboring gene STARR-seq mESC enhancer starr_37570 Neighboring gene STARR-seq mESC enhancer starr_37571 Neighboring gene STARR-seq mESC enhancer starr_37572 Neighboring gene FSHD region gene 2 family member 8

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Targeted (1)  1 citation

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within auditory behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within auditory receptor cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within axonogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within camera-type eye development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cochlea development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within inner ear morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within innervation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lens development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within linear vestibuloocular reflex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron projection morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within startle response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    acts_upstream_of_or_within vestibular reflex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within vestibulocochlear nerve development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within visual perception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell periphery IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    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
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    SLIT and NTRK-like protein 6
    Names
    neuronal transmembrane protein Slitrk6
    slit and trk like gene 6

    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.

    mRNA and Protein(s)

    1. NM_175499.4NP_780708.1  SLIT and NTRK-like protein 6 precursor

      See identical proteins and their annotated locations for NP_780708.1

      Status: VALIDATED

      Source sequence(s)
      AK029275, AK044796, BB374017, BC138664
      Consensus CDS
      CCDS27326.1
      UniProtKB/Swiss-Prot
      Q8BLL0, Q8C110
      UniProtKB/TrEMBL
      A6H6M2
      Related
      ENSMUSP00000077492.3, ENSMUST00000078386.4
      Conserved Domains (6) summary
      smart00082
      Location:516566
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:210222
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:94113
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:388426
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:387444
      LRR_8; Leucine rich repeat
      cl15307
      Location:218268
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000080.7 Reference GRCm39 C57BL/6J

      Range
      110984770..110992640 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006519009.5XP_006519072.1  SLIT and NTRK-like protein 6 isoform X1

      Conserved Domains (5) summary
      smart00082
      Location:493543
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:187199
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:7190
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:364421
      LRR_8; Leucine rich repeat
      cl15307
      Location:195245
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain