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Aliases for SKIV2L2 Gene

Aliases for SKIV2L2 Gene

  • Ski2 Like RNA Helicase 2 2 3 5
  • KIAA0052 2 3 4
  • Functional Spliceosome-Associated Protein 118 2 3
  • ATP-Dependent RNA Helicase SKIV2L2 3 4
  • ATP-Dependent RNA Helicase DOB1 3 4
  • TRAMP-Like Complex Helicase 3 4
  • Dob1 3 4
  • Mtr4 3 4
  • Superkiller Viralicidic Activity 2-Like 2 (S. Cerevisiae) 2
  • Superkiller Viralicidic Activity 2-Like 2 3
  • ATP-Dependent Helicase SKIV2L2 3
  • EC 3.6.4.13 4
  • EC 3.6.1 61
  • FSAP118 3

External Ids for SKIV2L2 Gene

Previous HGNC Symbols for SKIV2L2 Gene

  • KIAA0052

Previous GeneCards Identifiers for SKIV2L2 Gene

  • GC05P054640
  • GC05P051576
  • GC05P054605

Summaries for SKIV2L2 Gene

GeneCards Summary for SKIV2L2 Gene

SKIV2L2 (Ski2 Like RNA Helicase 2) is a Protein Coding gene. Among its related pathways are rRNA processing in the nucleus and cytosol and Deadenylation-dependent mRNA decay. GO annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is DDX60.

UniProtKB/Swiss-Prot for SKIV2L2 Gene

  • 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 SKIV2L2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SKIV2L2 Gene

Genomics for SKIV2L2 Gene

Regulatory Elements for SKIV2L2 Gene

Enhancers for SKIV2L2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G055436 1.5 Ensembl ENCODE dbSUPER 19.4 +131.1 131143 4.0 ATF1 PKNOX1 SIN3A GATA2 FOS SP3 CREB3 ZNF610 SMARCA4 PBX2 RNF138P1 SKIV2L2 PLPP1 DHX29 CCNO GC05M055421 ENSG00000279883
GH05G055711 1.1 ENCODE 10.6 +404.7 404677 2.0 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF766 ZNF207 DDX4 IL31RA SKIV2L2 DHX29 SLC38A9 RNA5SP183 GC05P055648
GH05G055632 1.2 Ensembl ENCODE dbSUPER 9.7 +328.0 327995 6.5 MAX NR3C1 RAD21 ATF2 NR2F2 RFX5 YY1 FOXA1 JUND ATF3 PLPP1 RNF138P1 SKIV2L2 DHX29 SLC38A9 DDX4 GC05P055648 LOC105378975
GH05G055305 1.1 ENCODE 10.1 -0.2 -232 4.6 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SKIV2L2 CCNO RNF138P1 DHX29 GC05P055257
GH05G055389 0.9 ENCODE 10.3 +83.3 83305 3.6 HDAC1 CBX3 ATF1 TBL1XR1 CREB3L1 FEZF1 RAD21 CHAMP1 YY1 TCF12 DHX29 SKIV2L2 CCNO RNF138P1 LOC100419851 GC05M055421
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SKIV2L2 on UCSC Golden Path with GeneCards custom track

Promoters for SKIV2L2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000180740 152 3001 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1

Genomic Location for SKIV2L2 Gene

Chromosome:
5
Start:
55,307,748 bp from pter
End:
55,425,581 bp from pter
Size:
117,834 bases
Orientation:
Plus strand

Genomic View for SKIV2L2 Gene

Genes around SKIV2L2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SKIV2L2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SKIV2L2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SKIV2L2 Gene

Proteins for SKIV2L2 Gene

  • Protein details for SKIV2L2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P42285-SK2L2_HUMAN
    Recommended name:
    Superkiller viralicidic activity 2-like 2
    Protein Accession:
    P42285
    Secondary Accessions:
    • Q2M386
    • Q6MZZ8
    • Q6P170
    • Q8N5R0
    • Q8TAG2

    Protein attributes for SKIV2L2 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 (SKIV2L2/MTR4), 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.
    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 SKIV2L2 Gene

Selected DME Specific Peptides for SKIV2L2 Gene

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

Post-translational modifications for SKIV2L2 Gene

  • Ubiquitination at Lys192, Lys587, Lys852, isoforms=873, and Lys1022
  • Modification sites at PhosphoSitePlus

Other Protein References for SKIV2L2 Gene

Domains & Families for SKIV2L2 Gene

Gene Families for SKIV2L2 Gene

Suggested Antigen Peptide Sequences for SKIV2L2 Gene

Graphical View of Domain Structure for InterPro Entry

P42285

UniProtKB/Swiss-Prot:

SK2L2_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 SKIV2L2: view

Function for SKIV2L2 Gene

Molecular function for SKIV2L2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for SKIV2L2 Gene

Gene Ontology (GO) - Molecular Function for SKIV2L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IDA 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 SKIV2L2: view
genes like me logo Genes that share phenotypes with SKIV2L2: view

Animal Model Products

CRISPR Products

miRNA for SKIV2L2 Gene

miRTarBase miRNAs that target SKIV2L2

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SKIV2L2 Gene

Localization for SKIV2L2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SKIV2L2 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 SKIV2L2 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SKIV2L2 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 SKIV2L2: view

Pathways & Interactions for SKIV2L2 Gene

genes like me logo Genes that share pathways with SKIV2L2: view

Gene Ontology (GO) - Biological Process for SKIV2L2 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 SKIV2L2: view

No data available for SIGNOR curated interactions for SKIV2L2 Gene

Drugs & Compounds for SKIV2L2 Gene

(3) Drugs for SKIV2L2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for SKIV2L2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with SKIV2L2: view

Transcripts for SKIV2L2 Gene

Unigene Clusters for SKIV2L2 Gene

Superkiller viralicidic activity 2-like 2 (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SKIV2L2 Gene

No ASD Table

Relevant External Links for SKIV2L2 Gene

GeneLoc Exon Structure for
SKIV2L2
ECgene alternative splicing isoforms for
SKIV2L2

Expression for SKIV2L2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SKIV2L2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SKIV2L2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.5) and Lymph node (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SKIV2L2 Gene



Protein tissue co-expression partners for SKIV2L2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SKIV2L2 Gene:

SKIV2L2

SOURCE GeneReport for Unigene cluster for SKIV2L2 Gene:

Hs.274531

Evidence on tissue expression from TISSUES for SKIV2L2 Gene

  • Nervous system(4.9)
  • Blood(4.3)
  • Kidney(4.3)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with SKIV2L2: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SKIV2L2 Gene

Orthologs for SKIV2L2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SKIV2L2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SKIV2L2 34 35
  • 99.84 (n)
cow
(Bos Taurus)
Mammalia SKIV2L2 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SKIV2L2 34 35
  • 94.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SKIV2L2 35
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SKIV2L2 35
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Skiv2l2 34
  • 89.83 (n)
mouse
(Mus musculus)
Mammalia Skiv2l2 34 16 35
  • 88.37 (n)
chicken
(Gallus gallus)
Aves SKIV2L2 34 35
  • 81.6 (n)
lizard
(Anolis carolinensis)
Reptilia SKIV2L2 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia skiv2l2 34
  • 77.22 (n)
zebrafish
(Danio rerio)
Actinopterygii skiv2l2 34 35
  • 73.3 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(2)35Df 34 35
  • 61.03 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009600 34
  • 58.23 (n)
worm
(Caenorhabditis elegans)
Secernentea mtr-4 34 35
  • 57.12 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MTR4 34 35 37
  • 59.64 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01364g 34
  • 58.61 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL181C 34
  • 56.57 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G59760 34
  • 58.67 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mtr4 34
  • 60.88 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8524 35
  • 60 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU03363 34
  • 53.41 (n)
Species where no ortholog for SKIV2L2 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 SKIV2L2 Gene

ENSEMBL:
Gene Tree for SKIV2L2 (if available)
TreeFam:
Gene Tree for SKIV2L2 (if available)

Paralogs for SKIV2L2 Gene

Paralogs for SKIV2L2 Gene

(2) SIMAP similar genes for SKIV2L2 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with SKIV2L2: view

Variants for SKIV2L2 Gene

Sequence variations from dbSNP and Humsavar for SKIV2L2 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000025009 -- 55,381,308(+) TGTTC(-/T)TTTTT intron-variant
rs1000057517 -- 55,390,455(+) GAACT(A/T)ACTTT intron-variant
rs1000065622 -- 55,338,787(+) TTTTC(-/TTTTTTTTTTTT)TTTTT intron-variant
rs1000112600 -- 55,377,462(+) AAAAT(A/G)TGAAA intron-variant, nc-transcript-variant
rs1000133028 -- 55,345,752(+) ACTTT(C/G)TGCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SKIV2L2 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 SKIV2L2 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)

Relevant External Links for SKIV2L2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SKIV2L2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SKIV2L2 Gene

Disorders for SKIV2L2 Gene

Relevant External Links for SKIV2L2

Genetic Association Database (GAD)
SKIV2L2
Human Genome Epidemiology (HuGE) Navigator
SKIV2L2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SKIV2L2

No disorders were found for SKIV2L2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SKIV2L2 Gene

Publications for SKIV2L2 Gene

  1. Interaction profiling identifies the human nuclear exosome targeting complex. (PMID: 21855801) Lubas M. … Jensen T.H. (Mol. Cell 2011) 2 3 4 64
  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. (Biochem. Biophys. Res. Commun. 2006) 2 3 4 64
  3. Several regions in the major histocompatibility complex confer risk for anti-CCP-antibody positive rheumatoid arthritis, independent of the DRB1 locus. (PMID: 18309376) Lee H.S. … Gregersen P.K. (Mol. Med. 2008) 3 46 64
  4. C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing. (PMID: 17412707) Schilders G. … Pruijn G.J.M. (Nucleic Acids Res. 2007) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for SKIV2L2 Gene

Sources for SKIV2L2 Gene

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