Mtrex Mtr4 exosome RNA helicase [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Mtrexprovided by MGI
Official Full Name: Mtr4 exosome RNA helicaseprovided by MGI
Primary source: MGI:MGI:1919448
See related: Ensembl:ENSMUSG00000016018 AllianceGenome:MGI:1919448
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Skiv2l2; mKIAA0052; 2610528A15Rik
Summary: Predicted to enable ATP binding activity and RNA helicase activity. Predicted to be involved in DNA damage response; RNA catabolic process; and maturation of 5.8S rRNA. Predicted to be located in nucleoplasm. Predicted to be part of TRAMP complex; catalytic step 2 spliceosome; and nuclear exosome (RNase complex). Is expressed in medial ganglionic eminence. Orthologous to human MTREX (Mtr4 exosome RNA helicase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E11.5 (RPKM 25.7), CNS E14 (RPKM 16.5) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 D2.2; 13 63.93 cM

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (113004306..113063914, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (112867780..112927380, complement)

Chromosome 13 - NC_000079.7 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 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?

Skiv2l2 knockdown cells accumulated replication-dependent histone mRNAs, among other RNAs, that could impede mitotic progression and indirectly trigger differentiation.
Title: Loss of the RNA helicase SKIV2L2 impairs mitotic progression and replication-dependent histone mRNA turnover in murine cell lines.
Study reports that the noncoding RNA processing activity of RNA exosome, a 3'-5' RNA exonuclease, controls sense and antisense strand DNA mutagenesis, and prevents an increased asymmetric mutagenesis burden using a mechanism that relies on the unexpected DNA/RNA hybrid unwinding activities of the Mtr4 and senataxin RNA helicases.
Title: Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry.
Results identify novel role for Mtr4 in targeting the 5' leader sequences of microRNAs for degradation.
Title: Certain adenylated non-coding RNAs, including 5' leader sequences of primary microRNA transcripts, accumulate in mouse cells following depletion of the RNA helicase MTR4.
SKIV2L2 is an RNA-binding protein localized to the nucleus in the round spermatids of mice
Title: Localization of a novel RNA-binding protein, SKIV2L2, to the nucleus in the round spermatids of mice.

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Variation

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Alleles

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

Endonuclease-mediated (3)
Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
involved_in RNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in RNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in RNA catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in maturation of 5.8S rRNA	IBA Inferred from Biological aspect of Ancestor more info
involved_in maturation of 5.8S rRNA	IEA Inferred from Electronic Annotation more info
involved_in maturation of 5.8S rRNA	ISO Inferred from Sequence Orthology more info
involved_in rRNA processing	ISO Inferred from Sequence Orthology more info
involved_in rRNA processing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of TRAMP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of TRAMP complex	IEA Inferred from Electronic Annotation more info
part_of TRAMP complex	ISO Inferred from Sequence Orthology more info
part_of catalytic step 2 spliceosome	IEA Inferred from Electronic Annotation more info
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
part_of exosome (RNase complex)	ISO Inferred from Sequence Orthology more info
part_of nuclear exosome (RNase complex)	ISO Inferred from Sequence Orthology more info
part_of nuclear exosome (RNase complex)	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: exosome RNA helicase MTR4

Names: ATP-dependent helicase SKIV2L2; TRAMP-like complex helicase; superkiller viralicidic activity 2-like 2

NP_082427.1

EC 3.6.4.13

XP_036014071.1

EC 3.6.4.13

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_028151.2 → NP_082427.1 exosome RNA helicase MTR4

See identical proteins and their annotated locations for NP_082427.1

Status: PROVISIONAL

Source sequence(s)

AC165265

Consensus CDS

CCDS26778.1

UniProtKB/Swiss-Prot

Q9CZU3

UniProtKB/TrEMBL

Q8BTX6

Related

ENSMUSP00000022281.4, ENSMUST00000022281.5

Conserved Domains (5) summary

COG4581
Location:92 → 1040

Dob10; Superfamily II RNA helicase [Replication, recombination and repair]

cd00079
Location:372 → 536

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00270
Location:142 → 285

DEAD; DEAD/DEAH box helicase

pfam08148
Location:866 → 1033

DSHCT; DSHCT (NUC185) domain

pfam13234
Location:582 → 838

rRNA_proc-arch; rRNA-processing arch domain

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_000079.7 Reference GRCm39 C57BL/6J

Range

113004306..113063914 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036158178.1 → XP_036014071.1 exosome RNA helicase MTR4 isoform X1

UniProtKB/TrEMBL

Q91YT4

Conserved Domains (1) summary

COG4581
Location:16 → 696

Dob10; Superfamily II RNA helicase [Replication, recombination and repair]