Human Gene SKIV2L2 (uc003jpy.4) Description and Page Index
  Description: Homo sapiens superkiller viralicidic activity 2-like 2 (S. cerevisiae) (SKIV2L2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:54,603,576-54,721,409 Size: 117,834 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr5:54,603,842-54,720,600 Size: 116,759 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:54,603,576-54,721,409)mRNA (may differ from genome)Protein (1042 aa)
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UniProtKBWikipedia

-  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;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SKIV2L2
CDC HuGE Published Literature: SKIV2L2

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -88.70266-0.333 Picture PostScript Text
3' UTR -193.79809-0.240 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
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  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
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

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: KIAA0052, Mtr4, NM_015360, NP_056175, P42285, Q2M386, Q6MZZ8, Q6P170, Q8N5R0, Q8TAG2, SK2L2_HUMAN
UCSC ID: uc003jpy.4
RefSeq Accession: NM_015360
Protein: P42285 (aka SK2L2_HUMAN)
CCDS: CCDS3967.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015360.4
exon count: 27CDS single in 3' UTR: no RNA size: 4222
ORF size: 3129CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5000.00frame shift in genome: no % Coverage: 99.57
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.