Aliases for MTREX Gene

Aliases for MTREX Gene

  • Mtr4 Exosome RNA Helicase 2 3 5
  • KIAA0052 2 3 4
  • Functional Spliceosome-Associated Protein 118 2 3
  • Superkiller Viralicidic Activity 2-Like 2 3 4
  • ATP-Dependent RNA Helicase SKIV2L2 3 4
  • ATP-Dependent RNA Helicase DOB1 3 4
  • TRAMP-Like Complex Helicase 3 4
  • Exosome RNA Helicase MTR4 3 4
  • Ski2 Like RNA Helicase 2 2 3
  • SKIV2L2 3 4
  • FSAP118 2 3
  • Dob1 2 3
  • Mtr4 2 3
  • Superkiller Viralicidic Activity 2-Like 2 (S. Cerevisiae) 2
  • ATP-Dependent Helicase SKIV2L2 3
  • EC 3.6.4.13 4
  • EC 3.6.1 51
  • MTREX 5
  • DOB1 4
  • MTR4 4

External Ids for MTREX Gene

Previous HGNC Symbols for MTREX Gene

  • KIAA0052
  • SKIV2L2

Summaries for MTREX Gene

GeneCards Summary for MTREX Gene

MTREX (Mtr4 Exosome RNA Helicase) is a Protein Coding gene. Diseases associated with MTREX include Posterior Myocardial Infarction and Robinow Syndrome, Autosomal Dominant 1. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. An important paralog of this gene is SKIV2L.

UniProtKB/Swiss-Prot Summary for MTREX Gene

  • Catalyzes the ATP-dependent unwinding of RNA duplexes with a single-stranded 3' RNA extension (PubMed:27871484, PubMed:29844170, PubMed:29906447). Central subunit of many protein complexes, namely TRAMP-like, nuclear exosome targeting (NEXT) and poly(A) tail exosome targeting (PAXT) (PubMed:27871484, PubMed:29844170, PubMed:21855801). NEXT functions as an RNA exosome cofactor that directs a subset of non-coding short-lived RNAs for exosomal degradation. NEXT is involved in surveillance and turnover of aberrant transcripts and non-coding RNAs (PubMed:27871484, PubMed:29844170). PAXT directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor ZCCHC8, which links to RNA-binding protein adapters (PubMed:27871484). Associated with the RNA exosome complex and involved in the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA (PubMed:17412707, PubMed:29107693). May be involved in pre-mRNA splicing. In the context of NEXT complex can also in vitro unwind DNA:RNA heteroduplexes with a 3' poly (A) RNA tracking strand (PubMed:29844170). Can promote unwinding and degradation of structured RNA substrates when associated with the nuclear exosome and its cofactors. Can displace a DNA strand while translocating on RNA to ultimately degrade the RNA within a DNA/RNA heteroduplex (PubMed:29906447).

Gene Wiki entry for MTREX Gene

Additional gene information for MTREX Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MTREX Gene

Genomics for MTREX Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MTREX Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MTREX on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MTREX

Genomic Locations for MTREX Gene

Genomic Locations for MTREX Gene
chr5:55,307,989-55,425,579
(GRCh38/hg38)
Size:
117,591 bases
Orientation:
Plus strand
chr5:54,603,576-54,721,409
(GRCh37/hg19)
Size:
117,834 bases
Orientation:
Plus strand

Genomic View for MTREX Gene

Genes around MTREX on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MTREX Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MTREX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MTREX Gene

Proteins for MTREX Gene

  • Protein details for MTREX Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P42285-MTREX_HUMAN
    Recommended name:
    Exosome RNA helicase MTR4
    Protein Accession:
    P42285
    Secondary Accessions:
    • Q2M386
    • Q6MZZ8
    • Q6P170
    • Q8N5R0
    • Q8TAG2

    Protein attributes for MTREX Gene

    Size:
    1042 amino acids
    Molecular mass:
    117805 Da
    Quaternary structure:
    • Component of a TRAMP-like complex, an ATP-dependent exosome regulatory complex consisting of a helicase (MTREX), an oligadenylate polymerase (TENT4B or TENT4A), and a substrate specific RNA-binding factor (ZCCHC7 or ZCCHC8). Several TRAMP-like complexes exist with specific compositions and are associated with nuclear, or nucleolar RNA exosomes (PubMed:21855801). Identified in the spliceosome C complex. Component of the poly(A) tail exosome targeting (PAXT) complex made of PABPN1, ZFC3H1 and MTREX that directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation (PubMed:27871484). Component of the nuclear exosome targeting (NEXT) complex composed of MTREX, ZCCHC8, and RBM7 that directs a subset of non-coding short-lived RNAs for exosomal degradation (PubMed:27905398, PubMed:27871484). Interacts with ZCCHC8; this interaction bridges the interaction between RBM7 and MTREX (PubMed:27905398, PubMed:16263084, PubMed:29844170, PubMed:31358741). Binds to ZFC3H1 and RBM7 in a RNase-insensitive manner (PubMed:27871484). Interacts with EXOSC10; the interaction mediates the association of MTREX with nuclear RNA exosomes (PubMed:26166824). Interacts with isoform 1 of NVL in an ATP-dependent manner; the interaction is required to associate NVL with nuclear RNA exosome (PubMed:16782053, PubMed:26166824, PubMed:11991638, PubMed:16263084, PubMed:21855801, PubMed:27871484, PubMed:27905398, PubMed:31358741). Interacts with WDR74; the interaction dissociation in a late stage of rRNA synthesis is required for appropriate maturation of pre-60S particles and depends on the ATPase activity of NVL (PubMed:26456651, PubMed:29107693). Interacts with MPHOSPH6 (PubMed:17412707). Interacts with the RNA cap-binding complex proteins NCBP1 and SRRT (PubMed:30842217). Interacts with NRDE2; the interaction is direct and negatively regulates MTREX function in exosomal degradation by changing its conformation precluding interaction with ZFC3H1, the RNA cap-binding complex proteins NCBP1 and SRRT, and association with the exosome (PubMed:30842217). Interacts with the nuclear RNA exosome complex (PubMed:29906447).
    SequenceCaution:
    • Sequence=AAH65258.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAA06124.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MTREX Gene

neXtProt entry for MTREX Gene

Selected DME Specific Peptides for MTREX Gene

P42285:
  • LFATETF
  • QMSGRAGR
  • MTTEILRSMLY
  • KGRVACEI
  • RDIVFAASLY
  • NNQSVLV

Post-translational modifications for MTREX Gene

  • Ubiquitination at Lys192, Lys587, Lys852, Lys873, and Lys1022
  • Modification sites at PhosphoSitePlus

Other Protein References for MTREX Gene

Domains & Families for MTREX Gene

Gene Families for MTREX Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for MTREX Gene

Suggested Antigen Peptide Sequences for MTREX Gene

GenScript: Design optimal peptide antigens:
  • SKIV2L2 protein (Q3MHC9_HUMAN)
  • ATP-dependent helicase SKIV2L2 (SK2L2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P42285

UniProtKB/Swiss-Prot:

MTREX_HUMAN :
  • Belongs to the helicase family. SKI2 subfamily.
Family:
  • Belongs to the helicase family. SKI2 subfamily.
genes like me logo Genes that share domains with MTREX: view

Function for MTREX Gene

Molecular function for MTREX Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the ATP-dependent unwinding of RNA duplexes with a single-stranded 3' RNA extension (PubMed:27871484, PubMed:29844170, PubMed:29906447). Central subunit of many protein complexes, namely TRAMP-like, nuclear exosome targeting (NEXT) and poly(A) tail exosome targeting (PAXT) (PubMed:27871484, PubMed:29844170, PubMed:21855801). NEXT functions as an RNA exosome cofactor that directs a subset of non-coding short-lived RNAs for exosomal degradation. NEXT is involved in surveillance and turnover of aberrant transcripts and non-coding RNAs (PubMed:27871484, PubMed:29844170). PAXT directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor ZCCHC8, which links to RNA-binding protein adapters (PubMed:27871484). Associated with the RNA exosome complex and involved in the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA (PubMed:17412707, PubMed:29107693). May be involved in pre-mRNA splicing. In the context of NEXT complex can also in vitro unwind DNA:RNA heteroduplexes with a 3' poly (A) RNA tracking strand (PubMed:29844170). Can promote unwinding and degradation of structured RNA substrates when associated with the nuclear exosome and its cofactors. Can displace a DNA strand while translocating on RNA to ultimately degrade the RNA within a DNA/RNA heteroduplex (PubMed:29906447).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13; Evidence={ECO:0000269|PubMed:29844170, ECO:0000269|PubMed:29906447};.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated when MTREX is incorporated into NEXT complex an the nuclear RNA exosome complex.

Enzyme Numbers (IUBMB) for MTREX Gene

Phenotypes From GWAS Catalog for MTREX Gene

Gene Ontology (GO) - Molecular Function for MTREX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0003724 RNA helicase activity IBA,IDA 29844170
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with MTREX: view
genes like me logo Genes that share phenotypes with MTREX: view

miRNA for MTREX Gene

miRTarBase miRNAs that target MTREX

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for MTREX Gene

Localization for MTREX Gene

Subcellular locations from UniProtKB/Swiss-Prot for MTREX Gene

Nucleus, nucleoplasm. Nucleus, nucleolus. Nucleus. Nucleus speckle.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MTREX gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 2
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for MTREX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000176 colocalizes_with nuclear exosome (RNase complex) IDA 26166824
GO:0000178 colocalizes_with exosome (RNase complex) IDA 11719186
GO:0005634 nucleus IBA,IDA 16263084
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
genes like me logo Genes that share ontologies with MTREX: view

Pathways & Interactions for MTREX Gene

genes like me logo Genes that share pathways with MTREX: view

Gene Ontology (GO) - Biological Process for MTREX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0000460 maturation of 5.8S rRNA IMP 17412707
GO:0006364 rRNA processing TAS --
GO:0006397 mRNA processing IEA --
GO:0006401 RNA catabolic process IDA 29906447
genes like me logo Genes that share ontologies with MTREX: view

No data available for SIGNOR curated interactions for MTREX Gene

Drugs & Compounds for MTREX Gene

(3) Drugs for MTREX Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

(1) Additional Compounds for MTREX Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Agonist, Full agonist, Partial agonist, Gating inhibitor, Antagonist 58-64-0
genes like me logo Genes that share compounds with MTREX: view

Transcripts for MTREX Gene

mRNA/cDNA for MTREX Gene

1 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for MTREX Gene

No ASD Table

Relevant External Links for MTREX Gene

GeneLoc Exon Structure for
MTREX

Expression for MTREX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MTREX

Evidence on tissue expression from TISSUES for MTREX Gene

  • Nervous system(4.9)
  • Blood(4.5)
  • Kidney(4.4)
  • Eye(4.2)
  • Skin(2.5)
  • Liver(2.2)
  • Heart(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with MTREX: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for MTREX Gene

Orthologs for MTREX Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for MTREX Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SKIV2L2 30 31
  • 99.84 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SKIV2L2 31
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SKIV2L2 30 31
  • 94.15 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SKIV2L2 31
  • 94 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SKIV2L2 31
  • 93 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Skiv2l2 30
  • 89.83 (n)
Mouse
(Mus musculus)
Mammalia Skiv2l2 30 31
  • 88.37 (n)
OneToOne
Mtrex 17
Chicken
(Gallus gallus)
Aves SKIV2L2 30 31
  • 81.6 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SKIV2L2 31
  • 87 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia skiv2l2 30
  • 77.22 (n)
Zebrafish
(Danio rerio)
Actinopterygii skiv2l2 30 31
  • 73.3 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta l(2)35Df 30 31
  • 61.03 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009600 30
  • 58.23 (n)
Worm
(Caenorhabditis elegans)
Secernentea mtr-4 30 31
  • 57.12 (n)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MTR4 30 31 33
  • 59.64 (n)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01364g 30
  • 58.61 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AEL181C 30
  • 56.57 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT1G59760 30
  • 58.67 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mtr4 30
  • 60.88 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.8524 31
  • 60 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU03363 30
  • 53.41 (n)
Species where no ortholog for MTREX was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for MTREX Gene

ENSEMBL:
Gene Tree for MTREX (if available)
TreeFam:
Gene Tree for MTREX (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MTREX: view image

Paralogs for MTREX Gene

Paralogs for MTREX Gene

genes like me logo Genes that share paralogs with MTREX: view

Variants for MTREX Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MTREX Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
689688 Uncertain Significance: Marfanoid habitus and intellectual disability 55,366,846(+) A/G MISSENSE_VARIANT
708819 Benign: not provided 55,308,070(+) T/G SYNONYMOUS_VARIANT
767998 Benign: not provided 55,400,298(+) A/G SYNONYMOUS_VARIANT
rs35643285 - p.Ala346Pro

Additional dbSNP identifiers (rs#s) for MTREX Gene

Structural Variations from Database of Genomic Variants (DGV) for MTREX Gene

Variant ID Type Subtype PubMed ID
esv2660955 CNV deletion 23128226
esv3413923 CNV duplication 20981092
esv3447783 CNV duplication 20981092
esv3605098 CNV loss 21293372
esv3605099 CNV loss 21293372
nsv1027090 CNV gain 25217958
nsv435812 CNV deletion 17901297
nsv478548 CNV novel sequence insertion 20440878
nsv518688 CNV loss 19592680
nsv523841 CNV loss 19592680
nsv598180 CNV gain 21841781
nsv598181 CNV loss 21841781
nsv823079 CNV loss 20364138

Variation tolerance for MTREX Gene

Residual Variation Intolerance Score: 9.66% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.98; 36.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MTREX Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MTREX

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MTREX Gene

Disorders for MTREX Gene

MalaCards: The human disease database

(3) MalaCards diseases for MTREX Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search MTREX in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with MTREX: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MTREX Gene

Publications for MTREX Gene

  1. Interaction profiling identifies the human nuclear exosome targeting complex. (PMID: 21855801) Lubas M … Jensen TH (Molecular cell 2011) 2 3 4
  2. The AAA-ATPase NVL2 is a component of pre-ribosomal particles that interacts with the DExD/H-box RNA helicase DOB1. (PMID: 16782053) Nagahama M … Tagaya M (Biochemical and biophysical research communications 2006) 2 3 4
  3. NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction. (PMID: 30842217) Wang J … Cheng H (Genes & development 2019) 3 4
  4. The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs. (PMID: 31358741) Lingaraju M … Conti E (Nature communications 2019) 3 4
  5. Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. (PMID: 29906447) Weick EM … Lima CD (Cell 2018) 3 4

Products for MTREX Gene

Sources for MTREX Gene