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Aliases for SKIV2L Gene

Aliases for SKIV2L Gene

  • Ski2 Like RNA Helicase 2 3 5
  • SKI2 Homolog, Superkiller Viralicidic Activity 2-Like 2 3
  • Helicase-Like Protein 3 4
  • SKIV2 3 4
  • DDX13 3 4
  • SKI2W 3 4
  • SKI2 3 4
  • HLP 3 4
  • Superkiller Viralicidic Activity 2 (S. Cerevisiae Homolog)-Like 2
  • Superkiller Viralicidic Activity 2-Like (S. Cerevisiae) 2
  • Superkiller Viralicidic Activity 2-Like 3
  • Helicase SKI2W 3
  • EC 3.6.4.- 4
  • EC 3.6.1 61
  • SKIV2L1 3
  • THES2 3
  • 170A 3
  • W 4

External Ids for SKIV2L Gene

Previous HGNC Symbols for SKIV2L Gene

  • SKIV2

Previous GeneCards Identifiers for SKIV2L Gene

  • GC06P031988
  • GC06P031697
  • GC06P032030
  • GC06P032034
  • GC06P031926
  • GC06P031713

Summaries for SKIV2L Gene

Entrez Gene Summary for SKIV2L Gene

  • DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a human homologue of yeast SKI2 and may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. This gene is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]

GeneCards Summary for SKIV2L Gene

SKIV2L (Ski2 Like RNA Helicase) is a Protein Coding gene. Diseases associated with SKIV2L include Trichohepatoenteric Syndrome 2 and Trichohepatoenteric Syndrome 1. Among its related pathways are Chaperonin-mediated protein folding and Deadenylation-dependent mRNA decay. GO annotations related to this gene include nucleic acid binding and helicase activity.

UniProtKB/Swiss-Prot for SKIV2L Gene

  • Helicase; has ATPase activity. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).

Gene Wiki entry for SKIV2L Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SKIV2L Gene

Genomics for SKIV2L Gene

Regulatory Elements for SKIV2L Gene

Enhancers for SKIV2L 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
GH06F031969 1.2 ENCODE 67 +12.8 12837 4.9 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 SKIV2L BRD2 DDX39B C4A BAG6 DXO ATF6B LY6G5B LSM2 CSNK2B
GH06F031907 1.3 Ensembl ENCODE 43.5 -49.2 -49204 5.2 PKNOX1 ARID4B GTF3C2 ZNF121 GLIS2 KLF7 FOS ZNF263 NFYC MXD4 SKIV2L VARS LY6G5B LSM2 C4A RNU6-850P DDX39B ATF6B CSNK2B GPANK1
GH06F031792 1.7 FANTOM5 Ensembl ENCODE 31.9 -163.1 -163110 6.7 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ATF6B BAG6 SKIV2L LSM2 LY6G5B DDX39B VARS MICA CSNK2B C4A
GH06F031928 1.3 Ensembl ENCODE 40.9 -29.4 -29378 1.3 PKNOX1 ZFP64 ARID4B SIN3A ZNF2 ZNF48 YY1 GLIS2 ZNF766 ZNF143 SKIV2L LY6G5B ATF6B DDX39B NFKBIL1 LSM2 PPT2 MIR1236 TCF19 STK19
GH06F031944 1.4 Ensembl ENCODE 35.3 -11.3 -11266 6.8 HDGF PKNOX1 ARNT CREB3L1 MLX ARID4B DMAP1 YY1 SLC30A9 FOS SKIV2L STK19B HLA-DRB1 ATF6B C4A HLA-DQA2 C2 STK19 EHMT2 ZBTB12
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SKIV2L on UCSC Golden Path with GeneCards custom track

Promoters for SKIV2L Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000025317 196 1601 CREB3L1 MLX DMAP1 YY1 ZNF143 ZNF263 SP3 MEF2D SSRP1 RCOR2

Genomic Location for SKIV2L Gene

Chromosome:
6
Start:
31,958,804 bp from pter
End:
31,969,755 bp from pter
Size:
10,952 bases
Orientation:
Plus strand

Genomic View for SKIV2L Gene

Genes around SKIV2L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SKIV2L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SKIV2L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for SKIV2L Gene

  • Protein details for SKIV2L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15477-SKIV2_HUMAN
    Recommended name:
    Helicase SKI2W
    Protein Accession:
    Q15477
    Secondary Accessions:
    • O15005
    • Q12902
    • Q15476
    • Q5ST66

    Protein attributes for SKIV2L Gene

    Size:
    1246 amino acids
    Molecular mass:
    137755 Da
    Quaternary structure:
    • Component of the SKI complex which consists of WDR61, SKIV2L and TTC37.
    SequenceCaution:
    • Sequence=AAB52523.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for SKIV2L Gene

Selected DME Specific Peptides for SKIV2L Gene

Q15477:
  • LFATETF
  • MTTEILRSMLY
  • RDIVFAASLY
  • GLLTGDV

Post-translational modifications for SKIV2L Gene

  • Ubiquitination at Lys 84, Lys 316, Lys 363, Lys 516, Lys 539, Lys 720, Lys 736, Lys 791, Lys 837, Lys 991, Lys 1004, Lys 1026, Lys 1075, and Lys 1225
  • Modification sites at PhosphoSitePlus

Other Protein References for SKIV2L Gene

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for SKIV2L

Domains & Families for SKIV2L Gene

Gene Families for SKIV2L Gene

Graphical View of Domain Structure for InterPro Entry

Q15477

UniProtKB/Swiss-Prot:

SKIV2_HUMAN :
  • Contains 1 helicase ATP-binding domain.
  • Belongs to the helicase family. SKI2 subfamily.
Domain:
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the helicase family. SKI2 subfamily.
genes like me logo Genes that share domains with SKIV2L: view

Function for SKIV2L Gene

Molecular function for SKIV2L Gene

GENATLAS Biochemistry:
superkiller viralicidic activity 2, (S cerevisiae homolog)-like 2,helicase recognized by monoclonal antibody 170A1 with homology to human KIAA052,(superfamily II)
UniProtKB/Swiss-Prot Function:
Helicase; has ATPase activity. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).

Enzyme Numbers (IUBMB) for SKIV2L Gene

Gene Ontology (GO) - Molecular Function for SKIV2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0003724 RNA helicase activity IEA --
GO:0004004 ATP-dependent RNA helicase activity TAS 7610041
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with SKIV2L: view
genes like me logo Genes that share phenotypes with SKIV2L: view

Human Phenotype Ontology for SKIV2L Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SKIV2L Gene

MGI Knock Outs for SKIV2L:

Animal Model Products

miRNA for SKIV2L Gene

miRTarBase miRNAs that target SKIV2L

Inhibitory RNA Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for SKIV2L Gene

Localization for SKIV2L Gene

Subcellular locations from UniProtKB/Swiss-Prot for SKIV2L Gene

Nucleus. Cytoplasm.

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 SKIV2L gene
Compartment Confidence
cytosol 5
nucleus 4
extracellular 2

Gene Ontology (GO) - Cellular Components for SKIV2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0055087 Ski complex IDA 16024656
genes like me logo Genes that share ontologies with SKIV2L: view

Pathways & Interactions for SKIV2L Gene

genes like me logo Genes that share pathways with SKIV2L: view

Gene Ontology (GO) - Biological Process for SKIV2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006401 RNA catabolic process IEA --
GO:0070478 nuclear-transcribed mRNA catabolic process, 3-5 exonucleolytic nonsense-mediated decay IBA --
genes like me logo Genes that share ontologies with SKIV2L: view

No data available for SIGNOR curated interactions for SKIV2L Gene

Drugs & Compounds for SKIV2L Gene

(1) Additional Compounds for SKIV2L Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SKIV2L: view

Transcripts for SKIV2L Gene

Unigene Clusters for SKIV2L Gene

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

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SKIV2L Gene

No ASD Table

Relevant External Links for SKIV2L Gene

GeneLoc Exon Structure for
SKIV2L
ECgene alternative splicing isoforms for
SKIV2L

Expression for SKIV2L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SKIV2L Gene

Protein differential expression in normal tissues from HIPED for SKIV2L Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.4), Lymph node (9.3), and Salivary gland (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SKIV2L Gene



Protein tissue co-expression partners for SKIV2L Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SKIV2L Gene:

SKIV2L

SOURCE GeneReport for Unigene cluster for SKIV2L Gene:

Hs.89864
genes like me logo Genes that share expression patterns with SKIV2L: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SKIV2L Gene

Orthologs for SKIV2L Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SKIV2L Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SKIV2L 34 35
  • 99.36 (n)
cow
(Bos Taurus)
Mammalia SKIV2L 34 35
  • 90.05 (n)
dog
(Canis familiaris)
Mammalia SKIV2L 34 35
  • 89.7 (n)
oppossum
(Monodelphis domestica)
Mammalia SKIV2L 35
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Skiv2l 34 16 35
  • 87.53 (n)
rat
(Rattus norvegicus)
Mammalia Skiv2l 34
  • 87.12 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SKIV2L 35
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves SKIV2L 35
  • 52 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SKIV2L 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia skiv2l 34
  • 60.57 (n)
zebrafish
(Danio rerio)
Actinopterygii skiv2l 34 35
  • 62.54 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003182 34
  • 54.37 (n)
fruit fly
(Drosophila melanogaster)
Insecta tst 36 34 35
  • 51.85 (n)
worm
(Caenorhabditis elegans)
Secernentea skih-2 34 35
  • 47.45 (n)
F01G4.3 36
  • 40 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER067C 34
  • 48.25 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SKI2 34 35 37
  • 47.76 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G46960 34
  • 50.42 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01857 34
  • 49.99 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC550.03c 34
  • 47.86 (n)
Species where no ortholog for SKIV2L 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)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SKIV2L Gene

ENSEMBL:
Gene Tree for SKIV2L (if available)
TreeFam:
Gene Tree for SKIV2L (if available)

Paralogs for SKIV2L Gene

(3) SIMAP similar genes for SKIV2L Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with SKIV2L: view

No data available for Paralogs for SKIV2L Gene

Variants for SKIV2L Gene

Sequence variations from dbSNP and Humsavar for SKIV2L Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs281875237 Trichohepatoenteric syndrome 2 (THES2) [MIM:614602], Pathogenic 31,962,012(+) AGTTG(G/T)GGCTG nc-transcript-variant, reference, missense
rs557829269 A colorectal cancer sample 31,966,801(+) GACAT(A/G)ATGAA nc-transcript-variant, reference, missense
VAR_035944 A breast cancer sample
rs200818962 Pathogenic 31,962,494(+) ACTTC(C/T)GAAAC nc-transcript-variant, reference, stop-gained
rs878853054 Uncertain significance 31,962,036(+) CCTGG(A/C)CCAGA nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SKIV2L Gene

Variant ID Type Subtype PubMed ID
nsv830628 CNV loss 17160897
nsv5247 CNV deletion 18451855
nsv428141 CNV gain+loss 18775914
nsv284 CNV deletion 15895083
nsv1126749 CNV deletion 24896259
nsv1112900 CNV deletion 24896259
nsv1073969 CNV deletion 25765185
esv2759415 CNV gain+loss 17122850
dgv10463n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
dgv10403n54 CNV loss 21841781

Variation tolerance for SKIV2L Gene

Residual Variation Intolerance Score: 7.75% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.35; 90.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SKIV2L Gene

Human Gene Mutation Database (HGMD)
SKIV2L
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SKIV2L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SKIV2L Gene

Disorders for SKIV2L Gene

MalaCards: The human disease database

(6) MalaCards diseases for SKIV2L Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
trichohepatoenteric syndrome 2
  • thes2
trichohepatoenteric syndrome 1
  • syndromic diarrhea
diarrhea
  • diarrhea of presumed infectious origin
macular degeneration, age-related, 7
  • macular degeneration, age-related, neovascular type
macular degeneration, age-related, 1
  • macular degeneration, age-related, reduced risk of
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SKIV2_HUMAN
  • Trichohepatoenteric syndrome 2 (THES2) [MIM:614602]: A syndrome characterized by intrauterine growth retardation, severe diarrhea in infancy requiring total parenteral nutrition, facial dysmorphism, immunodeficiency, and hair abnormalities, mostly trichorrhexis nodosa. Hepatic involvement contributes to the poor prognosis of affected patients. {ECO:0000269 PubMed:22444670}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SKIV2L

Genetic Association Database (GAD)
SKIV2L
Human Genome Epidemiology (HuGE) Navigator
SKIV2L
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SKIV2L
genes like me logo Genes that share disorders with SKIV2L: view

No data available for Genatlas for SKIV2L Gene

Publications for SKIV2L Gene

  1. Identification and characterization of a human cDNA homologous to yeast SKI2. (PMID: 7759100) Lee S.-G. … Song K. (Genomics 1995) 2 3 4 22 64
  2. Role of RDBP and SKIV2L variants in the major histocompatibility complex class III region in polypoidal choroidal vasculopathy etiology. (PMID: 19556007) Kondo N. … Negi A. (Ophthalmology 2009) 3 22 46 64
  3. Four ubiquitously expressed genes, RD (D6S45)-SKI2W (SKIV2L)-DOM3Z- RP1 (D6S60E), are present between complement component genes factor B and C4 in the class III region of the HLA. (PMID: 9799600) Yang Z. … Yu C.Y. (Genomics 1998) 2 3 22 64
  4. Human helicase gene SKI2W in the HLA class III region exhibits striking structural similarities to the yeast antiviral gene SKI2 and to the human gene KIAA0052: emergence of a new gene family. (PMID: 7610041) Dangel A.W. … Yu C.Y. (Nucleic Acids Res. 1995) 3 4 22 64
  5. SKIV2L mutations cause syndromic diarrhea, or trichohepatoenteric syndrome. (PMID: 22444670) Fabre A. … Badens C. (Am. J. Hum. Genet. 2012) 3 4 64

Products for SKIV2L Gene

Sources for SKIV2L Gene

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