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    Slitrk4 SLIT and NTRK-like family, member 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 302473, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Slitrk4provided by RGD
    Official Full Name
    SLIT and NTRK-like family, member 4provided by RGD
    Primary source
    RGD:1588563
    See related
    EnsemblRapid:ENSRNOG00000062783 AllianceGenome:RGD:1588563
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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 regulation of synapse organization. Predicted to act upstream of or within axonogenesis and positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in glutamatergic synapse. Orthologous to human SLITRK4 (SLIT and NTRK like family member 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Restricted expression toward (RPKM 134.4) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Slitrk4 in Genome Data Viewer
    Location:
    Xq36
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (147728163..147755086, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (142706495..142718968, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (147582195..147589529, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484007 Neighboring gene MAGE family member A9 Neighboring gene NOP2 nucleolar protein, pseudogene 1 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

    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. Slitrks control excitatory and inhibitory synapse formation with LAR receptor protein tyrosine phosphatases. Yim YS, et al. Proc Natl Acad Sci U S A, 2013 Mar 5. PMID 23345436, Free PMC Article
    2. 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
    3. Calsyntenins function as synaptogenic adhesion molecules in concert with neurexins. Um JW, et al. Cell Rep, 2014 Mar 27. PMID 24613359, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    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
    		  
    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 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
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    SLIT and NTRK-like protein 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_001106947.1 → NP_001100417.1  SLIT and NTRK-like protein 4 precursor

      See identical proteins and their annotated locations for NP_001100417.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474019
      UniProtKB/TrEMBL
      A0A8I6AET5, A6K517
      Related
      ENSRNOP00000092913.1, ENSRNOT00000003664.6
      Conserved Domains (5) summary
      sd00033
      Location:109 → 132
      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 → 532
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:531 → 563
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. NM_001433988.1 → NP_001420917.1  SLIT and NTRK-like protein 4 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A8I6AET5, A6K517

    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_086039.1 Reference GRCr8

      Range
      147728163..147755086 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279903.1 → XP_063135973.1  SLIT and NTRK-like protein 4 isoform X2

      Related
      ENSRNOP00000103889.1, ENSRNOT00000154017.1

    2. XM_039099600.2 → XP_038955528.1  SLIT and NTRK-like protein 4 isoform X1

      Related
      ENSRNOP00000112104.1, ENSRNOT00000156947.1
      Conserved Domains (5) summary
      sd00033
      Location:109 → 132
      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 → 532
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:531 → 563
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    3. XM_039099601.2 → XP_038955529.1  SLIT and NTRK-like protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AET5, A6K517
      Related
      ENSRNOP00000106515.1, ENSRNOT00000163623.1
      Conserved Domains (5) summary
      sd00033
      Location:109 → 132
      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 → 532
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:531 → 563
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
    Nucleotide Protein Strain
    Heading Accession and Version

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