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    Khdrbs2 KH RNA binding domain containing, signal transduction associated 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 170843, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Khdrbs2provided by RGD
    Official Full Name
    KH RNA binding domain containing, signal transduction associated 2provided by RGD
    Primary source
    RGD:621738
    See related
    EnsemblRapid:ENSRNOG00000012284 AllianceGenome:RGD:621738
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Slm1
    Summary
    Predicted to enable RNA binding activity and protein domain specific binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be active in nucleus. Orthologous to human KHDRBS2 (KH RNA binding domain containing, signal transduction associated 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 36.8) and Testes (RPKM 10.6) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Khdrbs2 in Genome Data Viewer
    Location:
    9q21
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (41943029..42449687)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (34447023..34953684)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (39501431..40008707, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 alpha 1, pseudogene 1 Neighboring gene U6 spliceosomal RNA Neighboring gene U7 small nuclear RNA Neighboring gene zinc finger protein 622 like 1 Neighboring gene FUS RNA binding protein, pseudogene 6

    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. p59(fyn)-mediated phosphorylation regulates the activity of the tissue-specific splicing factor rSLM-1. Stoss O, et al. Mol Cell Neurosci, 2004 Sep. PMID 15345239
    2. SAM68 regulates neuronal activity-dependent alternative splicing of neurexin-1. Iijima T, et al. Cell, 2011 Dec 23. PMID 22196734, Free PMC Article
    3. Characterization of Sam68-like mammalian proteins SLM-1 and SLM-2: SLM-1 is a Src substrate during mitosis. Di Fruscio M, et al. Proc Natl Acad Sci U S A, 1999 Mar 16. PMID 10077576, Free PMC Article
    4. Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA. Heinrich B, et al. J Biol Chem, 2009 May 22. PMID 19282290, Free PMC Article
    5. Next-generation sequencing to generate interactome datasets. Yu H, et al. Nat Methods, 2011 Jun. PMID 21516116, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SLM-1 is a tissue-specific splicing factor whose activity is regulated by tyrosine phosphorylation signals emanating from p59(fyn).
      Title: p59(fyn)-mediated phosphorylation regulates the activity of the tissue-specific splicing factor rSLM-1.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables SH2 domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables SH3 domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables poly(A) binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables poly(A) binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly(U) RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    KH domain-containing, RNA-binding, signal transduction-associated protein 2
    Names
    KH domain containing, RNA binding, signal transduction associated 2
    SLM-1
    Sam68-like mammalian protein 1
    rSLM-1

    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_133318.2 → NP_579852.1  KH domain-containing, RNA-binding, signal transduction-associated protein 2

      See identical proteins and their annotated locations for NP_579852.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q920F3
      UniProtKB/TrEMBL
      A6IN86
      Related
      ENSRNOP00000016579.3, ENSRNOT00000016578.7
      Conserved Domains (3) summary
      cd02395
      Location:61 → 180
      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:6 → 57
      Qua1; Qua1 domain
      pfam16568
      Location:271 → 321
      Sam68-YY; Tyrosine-rich domain of Sam68

    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_086027.1 Reference GRCr8

      Range
      41943029..42449687
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039082989.2 → XP_038938917.1  KH domain-containing, RNA-binding, signal transduction-associated protein 2 isoform X1

      Related
      ENSRNOP00000100781.1, ENSRNOT00000154861.1
      Conserved Domains (3) summary
      pfam16274
      Location:5 → 57
      Qua1; Qua1 domain
      pfam16568
      Location:271 → 321
      Sam68-YY; Tyrosine-rich domain of Sam68
      cd22469
      Location:54 → 171
      KH-I_KHDRBS2; type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins

    RNA

    1. XR_010054563.1 RNA Sequence

    2. XR_005488845.2 RNA Sequence

    3. XR_010054564.1 RNA Sequence

    4. XR_005488846.2 RNA Sequence

    5. XR_005488844.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q920F3.1 GenPept UniProtKB/Swiss-Prot:Q920F3

    Gene LinkOut

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

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