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    Slitrk2 SLIT and NTRK-like family, member 2 [ Mus musculus (house mouse) ]

    Gene ID: 245450, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Slitrk2provided by MGI
    Official Full Name
    SLIT and NTRK-like family, member 2provided by MGI
    Primary source
    MGI:MGI:2679449
    See related
    Ensembl:ENSMUSG00000036790 AllianceGenome:MGI:2679449
    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
    A930040J07
    Summary
    Involved in positive regulation of synapse assembly. Acts upstream of or within axonogenesis. Predicted to be located in dendrite and plasma membrane. Predicted to be active in GABA-ergic synapse; glutamatergic synapse; and postsynaptic membrane. Is expressed in several structures, including central nervous system; peripheral nervous system; retina; and trigeminal nerve. Used to study non-syndromic X-linked intellectual developmental disorder 111. 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 frontal lobe adult (RPKM 2.2), cortex adult (RPKM 2.1) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Slitrk2 in Genome Data Viewer
    Location:
    X A7.1; X 34.81 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (65692535..65705008)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (66648951..66661402)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene H2A histone family member L1R, pseudogene Neighboring gene predicted gene, 30914 Neighboring gene STARR-seq mESC enhancer starr_47287 Neighboring gene STARR-seq mESC enhancer starr_47288 Neighboring gene STARR-seq mESC enhancer starr_47289 Neighboring gene STARR-seq mESC enhancer starr_47290 Neighboring gene STARR-seq mESC enhancer starr_47291 Neighboring gene STARR-seq mESC enhancer starr_47292 Neighboring gene predicted gene, 57681 Neighboring gene predicted gene, 23000

    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
    • 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. Slitrk2 deficiency causes hyperactivity with altered vestibular function and serotonergic dysregulation. Katayama KI, et al. iScience, 2022 Jul 15. PMID 35789858, Free PMC Article
    2. SLITRK2 variants associated with neurodevelopmental disorders impair excitatory synaptic function and cognition in mice. El Chehadeh S, et al. Nat Commun, 2022 Jul 15. PMID 35840571, Free PMC Article
    3. 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
    4. Opposite Control of Excitatory and Inhibitory Synapse Formation by Slitrk2 and Slitrk5 on Dopamine Neurons Modulates Hyperactivity Behavior. Salesse C, et al. Cell Rep, 2020 Feb 18. PMID 32075770
    5. Differential expression of Slitrk family members in the mouse nervous system. Beaubien F, et al. Dev Dyn, 2009 Dec. PMID 19924824

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Opposite Control of Excitatory and Inhibitory Synapse Formation by Slitrk2 and Slitrk5 on Dopamine Neurons Modulates Hyperactivity Behavior.
      Title: Opposite Control of Excitatory and Inhibitory Synapse Formation by Slitrk2 and Slitrk5 on Dopamine Neurons Modulates Hyperactivity Behavior.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in 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 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic membrane adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in GABA-ergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in postsynaptic membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    SLIT and NTRK-like protein 2
    Names
    slit and trk like gene 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_001161431.1 → NP_001154903.1  SLIT and NTRK-like protein 2 precursor

      See identical proteins and their annotated locations for NP_001154903.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AL831757, BC111888, BE864556, CJ163676, CO431035
      Consensus CDS
      CCDS30169.1
      UniProtKB/Swiss-Prot
      Q810C0, Q8BXL6
      UniProtKB/TrEMBL
      Q14DP8, Q14DT0
      Related
      ENSMUSP00000130057.2, ENSMUST00000166241.2
      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:208 → 370
      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_198863.2 → NP_942563.2  SLIT and NTRK-like protein 2 precursor

      See identical proteins and their annotated locations for NP_942563.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AL831757, BC111888, BE864556, CO431035
      Consensus CDS
      CCDS30169.1
      UniProtKB/Swiss-Prot
      Q810C0, Q8BXL6
      UniProtKB/TrEMBL
      Q14DP8, Q14DT0
      Related
      ENSMUSP00000044094.5, ENSMUST00000036043.5
      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:208 → 370
      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

    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
      65692535..65705008
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528016.3 → XP_006528079.1  SLIT and NTRK-like protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006528079.1

      UniProtKB/Swiss-Prot
      Q810C0, Q8BXL6
      UniProtKB/TrEMBL
      Q14DP8, Q14DT0
      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:208 → 370
      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_006528014.3 → XP_006528077.1  SLIT and NTRK-like protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006528077.1

      UniProtKB/Swiss-Prot
      Q810C0, Q8BXL6
      UniProtKB/TrEMBL
      Q14DP8, Q14DT0
      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:208 → 370
      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_036161953.1 → XP_036017846.1  SLIT and NTRK-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q810C0, Q8BXL6
      UniProtKB/TrEMBL
      Q14DP8, Q14DT0
      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:208 → 370
      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

    4. XM_030251337.2 → XP_030107197.1  SLIT and NTRK-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q810C0, Q8BXL6
      UniProtKB/TrEMBL
      Q14DP8, Q14DT0
      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:208 → 370
      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
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q810C0.1 GenPept UniProtKB/Swiss-Prot:Q810C0

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