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    Slitrk2 SLIT and NTRK-like family, member 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309349, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Slitrk2provided by RGD
    Official Full Name
    SLIT and NTRK-like family, member 2provided by RGD
    Primary source
    RGD:1561361
    See related
    EnsemblRapid:ENSRNOG00000011562 AllianceGenome:RGD:1561361
    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
    Also known as
    RGD1561361
    Summary
    Predicted to be involved in axonogenesis; regulation of synapse assembly; and synaptic membrane adhesion. Is active in postsynaptic membrane. Human ortholog(s) of this gene implicated in non-syndromic X-linked intellectual developmental disorder 111. Orthologous to human SLITRK2 (SLIT and NTRK like family member 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 66.9), Uterus (RPKM 10.1) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Slitrk2 in Genome Data Viewer
    Location:
    Xq37
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (150287418..150299832)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (145246448..145259983)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (151099388..151111816)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120099343 Neighboring gene developmental pluripotency-associated 4, pseudogene 6 Neighboring gene large ribosomal subunit protein eL15-like Neighboring gene alkaline phosphatase, tissue-nonspecific isozyme-like

    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. Slitrk1 is localized to excitatory synapses and promotes their development. Beaubien F, et al. Sci Rep, 2016 Jun 7. PMID 27273464, Free PMC Article
    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. 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
    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
    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 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 positive regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of presynapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of synapse organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synaptic membrane adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in GABA-ergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in postsynaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SLIT and NTRK-like protein 2

    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_001107587.2 → NP_001101057.1  SLIT and NTRK-like protein 2 precursor

      See identical proteins and their annotated locations for NP_001101057.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6K520, D3ZK41
      Conserved Domains (6) summary
      smart00082
      Location:530 → 580
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:67 → 87
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:90 → 111
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:400 → 460
      LRR_8; Leucine rich repeat
      cd21340
      Location:358 → 531
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:216 → 252
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. NM_001434035.1 → NP_001420964.1  SLIT and NTRK-like protein 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6K520, D3ZK41

    3. NM_001434036.1 → NP_001420965.1  SLIT and NTRK-like protein 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6K520, D3ZK41

    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
      150287418..150299832
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006257626.5 → XP_006257688.1  SLIT and NTRK-like protein 2 isoform X1

      Conserved Domains (6) summary
      smart00082
      Location:530 → 580
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:67 → 87
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:90 → 111
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:400 → 460
      LRR_8; Leucine rich repeat
      cd21340
      Location:358 → 531
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:216 → 252
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. XM_017602027.3 → XP_017457516.1  SLIT and NTRK-like protein 2 isoform X1

      Related
      ENSRNOP00000088481.1, ENSRNOT00000108501.2
      Conserved Domains (6) summary
      smart00082
      Location:530 → 580
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:67 → 87
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:90 → 111
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:400 → 460
      LRR_8; Leucine rich repeat
      cd21340
      Location:358 → 531
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:216 → 252
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    3. XM_063279973.1 → XP_063136043.1  SLIT and NTRK-like protein 2 isoform X1

      UniProtKB/TrEMBL
      A6K520, D3ZK41
      Related
      ENSRNOP00000015401.6, ENSRNOT00000015401.8
    Nucleotide Protein Strain
    Heading Accession and Version

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