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

Gene ID: 170843, updated on 18-Sep-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, Apr 2022]
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 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 IEA
Inferred from Electronic Annotation
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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