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

Summary

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, Dec 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

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_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
(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.
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.
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.
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.
10 target mRNA substrates from testis extract are bound by T-STAR.
Title: Identification of messenger RNA substrates for mouse T-STAR.
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.

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Variation

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Alleles

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

Endonuclease-mediated (1)
Targeted (8) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Khdrbs3 (e-PCR), detects polymorphism
- UniSTS:547847

D15Mit3 (e-PCR), detects polymorphism
- UniSTS:127651

Khdrbs3 (e-PCR), detects polymorphism
- UniSTS:479171

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)

NM_001411210.1 → NP_001398139.1 KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform 2

Status: VALIDATED

Source sequence(s)

AC123936
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

NR_177197.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC123936
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

NC_000081.7 Reference GRCm39 C57BL/6J

Range

68800155..68973064

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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