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    SLITRK6 SLIT and NTRK like family member 6 [ Homo sapiens (human) ]

    Gene ID: 84189, updated on 9-Dec-2024

    Summary

    Official Symbol
    SLITRK6provided by HGNC
    Official Full Name
    SLIT and NTRK like family member 6provided by HGNC
    Primary source
    HGNC:HGNC:23503
    See related
    Ensembl:ENSG00000184564 MIM:609681; AllianceGenome:HGNC:23503
    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
    DFNMYP
    Summary
    This gene encodes a member of the SLITRK protein family. Members of this family are integral membrane proteins that are characterized by two N-terminal leucine-rich repeat (LRR) domains and a C-terminal region that shares homology with trk neurotrophin receptors. This protein functions as a regulator of neurite outgrowth required for normal hearing and vision. Mutations in this gene are a cause of myopia and deafness. [provided by RefSeq, Dec 2014]
    Expression
    Biased expression in urinary bladder (RPKM 12.2), salivary gland (RPKM 7.4) and 11 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See SLITRK6 in Genome Data Viewer
    Location:
    13q31.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (85792790..85799419, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (85041234..85047862, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (86366925..86373554, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 351 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:86006193-86006693 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:86182343-86182998 Neighboring gene NANOG hESC enhancer GRCh37_chr13:86193480-86193991 Neighboring gene RNA, U6 small nuclear 72, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:86238925-86240124 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:86428461-86428657 Neighboring gene Sharpr-MPRA regulatory region 1723 Neighboring gene MOB kinase activator 1A pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr13:86736088-86736589 Neighboring gene DEAD-box helicase 6 pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    High myopia-sensorineural deafness syndrome
    MedGen: C3806275 OMIM: 221200 GeneReviews: Deafness and Myopia Syndrome
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of irritable vs. elated mania suggests genetic differences between clinical subtypes of bipolar disorder.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC119595, MGC119596, MGC119597

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in adult locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in auditory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in auditory receptor cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cochlea development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in innervation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lens development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in linear vestibuloocular reflex IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in startle response IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vestibulocochlear nerve development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cell surface IDA
    Inferred from Direct Assay
    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
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    SLIT and NTRK-like protein 6
    Names
    4832410J21Rik
    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.

    Genomic

    1. NG_041801.2 RefSeqGene

      Range
      12265..18894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1357

    mRNA and Protein(s)

    1. NM_032229.3NP_115605.2  SLIT and NTRK-like protein 6 precursor

      See identical proteins and their annotated locations for NP_115605.2

      Status: REVIEWED

      Source sequence(s)
      AL162373
      Consensus CDS
      CCDS41903.1
      UniProtKB/Swiss-Prot
      A8K9S8, Q495Q0, Q6AW93, Q9H5Y7, Q9HAA8, Q9NT60
      Related
      ENSP00000495507.1, ENST00000647374.2
      Conserved Domains (4) summary
      smart00082
      Location:517567
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:94113
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:411471
      LRR_8; Leucine rich repeat
      cl26793
      Location:69494
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      85792790..85799419 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      85041234..85047862 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)