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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
  • Ski2 Like RNA Helicase 2 2 3
  • SKIV2L2 3 4
  • Superkiller Viralicidic Activity 2-Like 2 (S. Cerevisiae) 2
  • ATP-Dependent Helicase SKIV2L2 3
  • Exosome RNA Helicase MTR4 3
  • EC 3.6.4.13 4
  • FSAP118 3
  • Dob1 3
  • Mtr4 3
  • 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. Among its related pathways are rRNA processing in the nucleus and cytosol and mRNA Splicing - Major Pathway. An important paralog of this gene is SKIV2L.

UniProtKB/Swiss-Prot for MTREX Gene

  • Component of exosome targeting complexes. Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that 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 MTREX, which links to RNA-binding protein adapters (PubMed:27871484). May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3-processing of the 7S pre-RNA to the mature 5.8S rRNA.

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 , fRNAdb sequence ontologies and piRNA Summary for MTREX Gene

Genomics for MTREX Gene

GeneHancer (GH) Regulatory Elements for MTREX Gene

Promoters and enhancers for MTREX Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J055305 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 692.1 -0.2 -232 4.6 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 MTREX DHX29 SLC38A9 ENSG00000264281 CCNO RNF138P1 GC05P055257
GH05J054516 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 32.7 -788.0 -787977 6.2 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF766 ZNF213 ZNF207 ZNF143 SNX18 PIR32129 MTREX DHX29 LOC100130990 HSPB3 PIR52196
GH05J055463 Enhancer 0.9 FANTOM5 64.2 +156.4 156355 0.3 ZNF493 ZFP64 MZF1 ZNF155 ZNF121 ZNF23 ZNF138 KLF7 ZNF202 ZNF680 DHX29 MTREX SLC38A9 GPX8 RNF138P1 ENSG00000264281 LOC100419851 FLJ31104 ENSG00000279883 GC05M055421
GH05J055226 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 26 -80.6 -80633 2.2 ARID4B SIN3A ZNF2 YY1 ZNF213 ZNF143 KLF13 SP3 REST SMARCB1 MCIDAS MTREX DHX29 SLC38A9 LOC105378973 ENSG00000249016 RNA5SP183 HNRNPH1P3 LINC01033 FLJ31104
GH05J054308 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.4 -997.6 -997577 4.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B ARL15 DHX29 MTREX LINC01033 LINC02105 ENSG00000249016 ENSG00000279638
- 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 UCSC Golden Path with GeneCards custom track

Genomic Locations for MTREX Gene

Genomic Locations for MTREX Gene
chr5:55,307,748-55,425,581
(GRCh38/hg38)
Size:
117,834 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 (PAPD5 or PAPD7), 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. Identified in the spliceosome C complex. Interacts with isoform 1 of NVL in an ATP-dependent manner. 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 (PubMed:27905398, PubMed:16263084). Binds to ZFC3H1 and RBM7 in a RNase-insensitive manner (PubMed:27871484).
    SequenceCaution:
    • Sequence=AAH65258.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA06124.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for MTREX Gene

Post-translational modifications for MTREX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for MTREX Gene

No data available for DME Specific Peptides for MTREX Gene

Domains & Families for MTREX Gene

Gene Families for MTREX Gene

Suggested Antigen Peptide Sequences for MTREX Gene

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:
Component of exosome targeting complexes. Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that 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 MTREX, which links to RNA-binding protein adapters (PubMed:27871484). May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3-processing of the 7S pre-RNA to the mature 5.8S rRNA.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

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:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0003724 RNA helicase activity IEA --
GO:0004004 ATP-dependent RNA helicase activity IBA --
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

Animal Model Products

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.

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
extracellular 2
cytosol 2
mitochondrion 1
peroxisome 1

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:0000178 colocalizes_with exosome (RNase complex) IDA 11719186
GO:0005634 nucleus IEA,IDA 16263084
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005730 nucleolus 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 IBA --
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, Full agonist, Antagonist, Potentiation, Pore Blocker 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
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with MTREX: view

Transcripts for MTREX Gene

mRNA/cDNA for MTREX Gene

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

No ASD Table

Relevant External Links for MTREX Gene

GeneLoc Exon Structure for
MTREX
ECgene alternative splicing isoforms for
MTREX

Expression for MTREX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of MTREX Gene:

MTREX

Evidence on tissue expression from TISSUES for MTREX Gene

  • Nervous system(4.9)
  • Blood(4.3)
  • Kidney(4.3)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with MTREX: view

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 34 33
  • 99.84 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SKIV2L2 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SKIV2L2 34 33
  • 94.15 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SKIV2L2 34
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SKIV2L2 34
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Skiv2l2 33
  • 89.83 (n)
mouse
(Mus musculus)
Mammalia Skiv2l2 16 34 33
  • 88.37 (n)
chicken
(Gallus gallus)
Aves SKIV2L2 34 33
  • 81.6 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SKIV2L2 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia skiv2l2 33
  • 77.22 (n)
zebrafish
(Danio rerio)
Actinopterygii skiv2l2 34 33
  • 73.3 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta l(2)35Df 34 33
  • 61.03 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009600 33
  • 58.23 (n)
worm
(Caenorhabditis elegans)
Secernentea mtr-4 34 33
  • 57.12 (n)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MTR4 36 34 33
  • 59.64 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01364g 33
  • 58.61 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL181C 33
  • 56.57 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G59760 33
  • 58.67 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mtr4 33
  • 60.88 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8524 34
  • 60 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU03363 33
  • 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 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 from dbSNP and Humsavar for MTREX Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000025009 -- 55,381,309(+) TTTTTT/TTTTTTT intron_variant
rs1000057517 -- 55,390,455(+) T/A intron_variant
rs1000112600 -- 55,377,462(+) A/G intron_variant
rs1000133028 -- 55,345,752(+) C/G intron_variant
rs1000204665 -- 55,321,645(+) G/C/T intron_variant

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

No disorders were found for MTREX Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links 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 58
  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 58
  3. Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts. (PMID: 27871484) Meola N … Jensen TH (Molecular cell 2016) 3 4 58
  4. Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors. (PMID: 27905398) Falk S … Conti E (Nature communications 2016) 3 4 58
  5. C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing. (PMID: 17412707) Schilders G … Pruijn GJ (Nucleic acids research 2007) 3 4 58

Products for MTREX Gene

Sources for MTREX Gene

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