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    Slitrk4 SLIT and NTRK-like family, member 4 [ Mus musculus (house mouse) ]

    Gene ID: 245446, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Slitrk4provided by MGI
    Official Full Name
    SLIT and NTRK-like family, member 4provided by MGI
    Primary source
    MGI:MGI:2442509
    See related
    Ensembl:ENSMUSG00000046699 AllianceGenome:MGI:2442509
    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
    6430513G13; D930039I09Rik
    Summary
    Acts upstream of or within axonogenesis and positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in glutamatergic synapse. Is expressed in several structures, including brain; ganglia; and spinal cord. Orthologous to human SLITRK4 (SLIT and NTRK like family member 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in frontal lobe adult (RPKM 2.1), cerebellum adult (RPKM 1.9) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Slitrk4 in Genome Data Viewer
    Location:
    X A7.1; X 34.57 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (63308489..63320951, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (64264883..64277345, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_47268 Neighboring gene predicted gene 6760 Neighboring gene MAGE family member A9 Neighboring gene DMRT-like family C1c2 pseudogene Neighboring gene predicted gene, 24598

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The SLITRK4-CNPY3 axis promotes liver metastasis of gastric cancer by enhancing the endocytosis and recycling of TrkB in tumour cells. Zhou YQ, et al. Cell Oncol (Dordr), 2023 Aug. PMID 37012514
    2. Structure of Slitrk2-PTPδ complex reveals mechanisms for splicing-dependent trans-synaptic adhesion. Yamagata A, et al. Sci Rep, 2015 May 19. PMID 25989451, Free PMC Article
    3. Differential expression of Slitrk family members in the mouse nervous system. Beaubien F, et al. Dev Dyn, 2009 Dec. PMID 19924824
    4. Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. Aruga J, et al. Gene, 2003 Oct 2. PMID 14557068
    5. Secreted TARSH regulates olfactory mitral cell dendritic complexity. Cheng TW, et al. Eur J Neurosci, 2009 Mar. PMID 19302145, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The SLITRK4-CNPY3 axis promotes liver metastasis of gastric cancer by enhancing the endocytosis and recycling of TrkB in tumour cells.
      Title: The SLITRK4-CNPY3 axis promotes liver metastasis of gastric cancer by enhancing the endocytosis and recycling of TrkB in tumour cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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 
    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 regulation of synapse organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    SLIT and NTRK-like protein 4
    Names
    slit and trk like gene 4

    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_001365111.1 → NP_001352040.1  SLIT and NTRK-like protein 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AL669956
      Consensus CDS
      CCDS30167.1
      UniProtKB/Swiss-Prot
      Q810B8, Q8BL56, Q8BWB0, Q8BYG4, Q8C056
      UniProtKB/TrEMBL
      Q149A4
      Conserved Domains (4) summary
      sd00033
      Location:63 → 84
      LRR_RI; leucine-rich repeat [structural motif]
      NF033189
      Location:15 → 253
      internalin_A; class 1 internalin InlA
      pfam13855
      Location:402 → 461
      LRR_8; Leucine rich repeat
      cd21340
      Location:359 → 550
      PPP1R42; protein phosphatase 1 regulatory subunit 42

    2. NM_001365112.1 → NP_001352041.1  SLIT and NTRK-like protein 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AK032263, AK053065, AL669956, BC079655, BC117891
      Consensus CDS
      CCDS30167.1
      UniProtKB/Swiss-Prot
      Q810B8, Q8BL56, Q8BWB0, Q8BYG4, Q8C056
      UniProtKB/TrEMBL
      Q149A4
      Related
      ENSMUSP00000110327.2, ENSMUST00000114679.2
      Conserved Domains (4) summary
      sd00033
      Location:63 → 84
      LRR_RI; leucine-rich repeat [structural motif]
      NF033189
      Location:15 → 253
      internalin_A; class 1 internalin InlA
      pfam13855
      Location:402 → 461
      LRR_8; Leucine rich repeat
      cd21340
      Location:359 → 550
      PPP1R42; protein phosphatase 1 regulatory subunit 42

    3. NM_178740.5 → NP_848855.2  SLIT and NTRK-like protein 4 precursor

      See identical proteins and their annotated locations for NP_848855.2

      Status: VALIDATED

      Source sequence(s)
      AK032263, AK053065, AL669956, BC079655
      Consensus CDS
      CCDS30167.1
      UniProtKB/Swiss-Prot
      Q810B8, Q8BL56, Q8BWB0, Q8BYG4, Q8C056
      UniProtKB/TrEMBL
      Q149A4
      Related
      ENSMUSP00000064443.8, ENSMUST00000069926.14
      Conserved Domains (4) summary
      sd00033
      Location:63 → 84
      LRR_RI; leucine-rich repeat [structural motif]
      NF033189
      Location:15 → 253
      internalin_A; class 1 internalin InlA
      pfam13855
      Location:402 → 461
      LRR_8; Leucine rich repeat
      cd21340
      Location:359 → 550
      PPP1R42; protein phosphatase 1 regulatory subunit 42

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      63308489..63320951 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036161952.1 → XP_036017845.1  SLIT and NTRK-like protein 4 isoform X1

      UniProtKB/Swiss-Prot
      Q810B8, Q8BL56, Q8BWB0, Q8BYG4, Q8C056
      UniProtKB/TrEMBL
      Q149A4
      Conserved Domains (4) summary
      sd00033
      Location:63 → 84
      LRR_RI; leucine-rich repeat [structural motif]
      NF033189
      Location:15 → 253
      internalin_A; class 1 internalin InlA
      pfam13855
      Location:402 → 461
      LRR_8; Leucine rich repeat
      cd21340
      Location:359 → 550
      PPP1R42; protein phosphatase 1 regulatory subunit 42
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q810B8.2 GenPept UniProtKB/Swiss-Prot:Q810B8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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