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

Gene ID: 13992, updated on 2-Nov-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 central nervous system; 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, Nov 2024]
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 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. Identification of messenger RNA substrates for mouse T-STAR. Zhang LY, et al. Biochemistry (Mosc), 2009 Nov. PMID 19916944
  2. Control of neuronal synapse specification by a highly dedicated alternative splicing program. Traunmüller L, et al. Science, 2016 May 20. PMID 27174676
  3. 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
  4. 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
  5. 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

See all (41) 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)
  • Endonuclease-mediated (1) 
  • Targeted (8)  1 citation

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 RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables SH3 domain binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein 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 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 IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
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

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