Human Gene MTREX (ENST00000230640.10_4) from GENCODE V47lift37

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Description: Mtr4 exosome RNA helicase (from RefSeq NM_015360.5)
Gencode Transcript: ENST00000230640.10_4
Gencode Gene: ENSG00000039123.16_9
Transcript (Including UTRs)
Position: hg19 chr5:54,603,817-54,721,407 Size: 117,591 Total Exon Count: 27 Strand: +
Coding Region
Position: hg19 chr5:54,603,842-54,720,600 Size: 116,759 Coding Exon Count: 27

Page Index	Sequence and Links	UniProtKB Comments	Primers	Gene Alleles	RNA-Seq Expression
Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations	mRNA Descriptions
Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr5:54,603,817-54,721,407)			mRNA (may differ from genome)		Protein (1042 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	MGI
OMIM	PubMed	Reactome	UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SK2L2_HUMAN DESCRIPTION: RecName: Full=Superkiller viralicidic activity 2-like 2; EC=3.6.4.13; AltName: Full=ATP-dependent helicase SKIV2L2; FUNCTION: 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. CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate. SUBUNIT: Associated with the RNA exosome complex. Identified in the spliceosome C complex. INTERACTION: Q99547:MPHOSPH6; NbExp=2; IntAct=EBI-347612, EBI-373187; SUBCELLULAR LOCATION: Nucleus, nucleolus. SIMILARITY: Belongs to the helicase family. SKI2 subfamily. SIMILARITY: Contains 1 helicase ATP-binding domain. SIMILARITY: Contains 1 helicase C-terminal domain. SEQUENCE CAUTION: Sequence=AAH65258.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA06124.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 22.44 RPKM in Cells - EBV-transformed lymphocytes Total median expression: 548.40 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-0.70	25	-0.028	Picture	PostScript	Text
3' UTR	-184.20	807	-0.228	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR012961 - DSH_C
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR016438 - RNA_helicase_ATP-dep_SK12/DOB1
IPR025696 - rRNA_proc-arch_dom

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain
PF08148 - DSHCT (NUC185) domain
PF13234 - rRNA-processing arch domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on P42285


Front	Top	Side

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Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	Genome Browser
Gene Details	Gene Details		Gene Details	Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase	SGD
				Protein Sequence	Protein Sequence
				Alignment	Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000166 nucleotide binding GO:0003676 nucleic acid binding GO:0003723 RNA binding GO:0003724 RNA helicase activity GO:0004004 ATP-dependent RNA helicase activity GO:0004386 helicase activity GO:0005515 protein binding GO:0005524 ATP binding GO:0016787 hydrolase activity Biological Process: GO:0000398 mRNA splicing, via spliceosome GO:0000460 maturation of 5.8S rRNA GO:0006364 rRNA processing GO:0006397 mRNA processing GO:0006401 RNA catabolic process GO:0008380 RNA splicing Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005681 spliceosomal complex GO:0005730 nucleolus GO:0071013 catalytic step 2 spliceosome GO:0000178 exosome (RNase complex)

Descriptions from all associated GenBank mRNAs


	BX640789 - Homo sapiens mRNA; cDNA DKFZp686K2075 (from clone DKFZp686K2075). BC104996 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone MGC:132656 IMAGE:8143999), complete cds. BC113509 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone MGC:142069 IMAGE:8322561), complete cds. BC028604 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone MGC:33192 IMAGE:4820164), complete cds. AK291649 - Homo sapiens cDNA FLJ76877 complete cds, highly similar to Homo sapiens superkiller viralicidic activity 2-like 2 (SKIV2L2), mRNA. AK304788 - Homo sapiens cDNA FLJ55446 complete cds, highly similar to Superkiller viralicidic activity 2-like 2 (EC 3.6.1.-). D29641 - Homo sapiens KIAA0052 mRNA for KIAA0052 protein. BC065258 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone IMAGE:6146338), partial cds. AB527662 - Synthetic construct DNA, clone: pF1KB0496, Homo sapiens SKIV2L2 gene for superkiller viralicidic activity 2-like 2, without stop codon, in Flexi system. KJ898500 - Synthetic construct Homo sapiens clone ccsbBroadEn_07894 SKIV2L2 gene, encodes complete protein. BC014669 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone IMAGE:4849317), partial cds. BC031779 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone IMAGE:4520464), partial cds. BC105291 - Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae), mRNA (cDNA clone IMAGE:6652652), partial cds. AF085966 - Homo sapiens full length insert cDNA clone YS84B07. AK123505 - Homo sapiens cDNA FLJ41511 fis, clone BRTHA2010008. JD105188 - Sequence 86212 from Patent EP1572962. JD347566 - Sequence 328590 from Patent EP1572962. JD042395 - Sequence 23419 from Patent EP1572962. CU691781 - Synthetic construct Homo sapiens gateway clone IMAGE:100021102 3' read PPAP2A mRNA. JD139329 - Sequence 120353 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein P42285 (Reactome details) participates in the following event(s): R-HSA-72163 mRNA Splicing - Major Pathway R-HSA-72172 mRNA Splicing R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA R-HSA-8868773 rRNA processing in the nucleus and cytosol R-HSA-8953854 Metabolism of RNA R-HSA-72312 rRNA processing

Other Names for This Gene


	Alternate Gene Symbols: DOB1 , ENST00000230640.1, ENST00000230640.2, ENST00000230640.3, ENST00000230640.4, ENST00000230640.5, ENST00000230640.6, ENST00000230640.7, ENST00000230640.8, ENST00000230640.9, KIAA0052, MTR4 , MTREX , MTREX_HUMAN, NM_015360, P42285, Q2M386, Q6MZZ8, Q6P170, Q8N5R0, Q8TAG2, SKIV2L2, uc317dte.1, uc317dte.2 UCSC ID: ENST00000230640.10_4 RefSeq Accession: NM_015360.5 Protein: P42285 (aka SK2L2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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