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    Khdrbs3 KH domain containing, RNA binding, signal transduction associated 3 [ Mus musculus (house mouse) ]

    Gene ID: 13992, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Khdrbs3provided by MGI
    Official Full Name
    KH domain containing, RNA binding, signal transduction associated 3provided by MGI
    Primary source
    MGI:MGI:1313312
    See related
    Ensembl:ENSMUSG00000022332 AllianceGenome:MGI:1313312
    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
    Etle; Salp; Slm2; SLM-2; T-STAR
    Summary
    Predicted to enable RNA binding activity; identical protein binding activity; and protein domain specific binding activity. Involved in regulation of mRNA splicing, via spliceosome. Located in nucleoplasm. Is expressed in several structures, including brain; genitourinary system; lung; sensory organ; and stomach. Orthologous to human KHDRBS3 (KH RNA binding domain containing, signal transduction associated 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in CNS E18 (RPKM 36.8), cortex adult (RPKM 31.0) and 19 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Khdrbs3 in Genome Data Viewer
    Location:
    15 D3; 15 30.36 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (68800155..68973064)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (68928392..69101794)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_38912 Neighboring gene predicted gene, 41341 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_38913 Neighboring gene predicted gene, 31550 Neighboring gene RIKEN cDNA 4930573C08 gene Neighboring gene RIKEN cDNA 4930504C09 gene

    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. A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior. Ehrmann I, et al. Cell Rep, 2016 Dec 20. PMID 28009295, Free PMC Article
    2. Control of neuronal synapse specification by a highly dedicated alternative splicing program. Traunmüller L, et al. Science, 2016 May 20. PMID 27174676
    3. Identification of messenger RNA substrates for mouse T-STAR. Zhang LY, et al. Biochemistry (Mosc), 2009 Nov. PMID 19916944
    4. Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control. Danilenko M, et al. Nucleic Acids Res, 2017 Apr 20. PMID 27994030, Free PMC Article
    5. Alternative splicing coupled nonsense-mediated decay generates neuronal cell type-specific expression of SLM proteins. Traunmüller L, et al. J Neurosci, 2014 Dec 10. PMID 25505328, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our data reveal a pathway of SLM2 homeostatic auto-regulation controlling brain network activity and behavior
      Title: A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior.
    2. (Nrxn) is a critical element in selective trans-synaptic interactions. This study evaluated the synaptogenic receptor activity of NL1/2/3 isoforms in a neuron-fibroblast co-culture system, in which the Nrxn AS4 segments are manipulated using SLM2, a selective and dominant regulator of AS4 splicing.
      Title: Neuroligin-induced presynaptic differentiation through SLM2-mediated splicing modifications of neurexin in cerebellar cultures.
    3. this study found that the RNA-binding protein SLM2 is essential for functional specification of glutamatergic synapses in the mouse hippocampus.
      Title: Control of neuronal synapse specification by a highly dedicated alternative splicing program.
    4. Sam68 and T-STAR could regulate alternative splicing of some pre-mRNAs by bringing two distant UAA motifs into proximity and looping out regions of the pre-mRNA.
      Title: Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.
    5. A hierarchical, SLM2-dependent mechanism in hippocampus was identified for cell type-specific expression of neuronal splicing regulators.
      Title: Alternative splicing coupled nonsense-mediated decay generates neuronal cell type-specific expression of SLM proteins.
    6. 10 target mRNA substrates from testis extract are bound by T-STAR.
      Title: Identification of messenger RNA substrates for mouse T-STAR.
    7. expression of active BRK/Sik results in increased SLM-1 and SLM-2 phosphorylation which has functional relevance and leads to inhibition of their RNA-binding
      Title: The nuclear tyrosine kinase BRK/Sik phosphorylates and inhibits the RNA-binding activities of the Sam68-like mammalian proteins SLM-1 and SLM-2.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (8)  1 citation
    • Endonuclease-mediated (1) 

    Pathways from PubChem

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    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 RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables SH3 domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of RNA splicing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    KH domain-containing, RNA-binding, signal transduction-associated protein 3
    Names
    RNA-binding protein Etoile
    etoile
    sam68-like mammalian 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_001411210.1 → NP_001398139.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC123936

    2. NM_010158.3 → NP_034288.2  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform 1

      See identical proteins and their annotated locations for NP_034288.2

      Status: VALIDATED

      Source sequence(s)
      AC123936
      Consensus CDS
      CCDS27513.1
      UniProtKB/Swiss-Prot
      O88624, Q9R226
      Related
      ENSMUSP00000022954.7, ENSMUST00000022954.7
      Conserved Domains (3) summary
      cd02395
      Location:58 → 177
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
      pfam16274
      Location:5 → 53
      Qua1; Qua1 domain
      pfam16568
      Location:266 → 320
      Sam68-YY; Tyrosine-rich domain of Sam68

    RNA

    1. NR_177197.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC123936

    2. NR_177198.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC123936

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      68800155..68973064
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036159122.1 → XP_036015015.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X1

      Conserved Domains (3) summary
      pfam16274
      Location:4 → 53
      Qua1; Qua1 domain
      pfam16568
      Location:266 → 308
      Sam68-YY; Tyrosine-rich domain of Sam68
      cd22470
      Location:48 → 160
      KH-I_KHDRBS3; type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9R226.1 GenPept UniProtKB/Swiss-Prot:Q9R226

    Gene LinkOut

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

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