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 fami... See more...

Aliases for SKIV2L Gene

Aliases for SKIV2L Gene

  • Ski2 Like RNA Helicase 2 3 5
  • DDX13 2 3 4
  • SKI2W 2 3 4
  • HLP 2 3 4
  • SKI2 Homolog, Superkiller Viralicidic Activity 2-Like 2 3
  • Helicase-Like Protein 3 4
  • Helicase SKI2W 3 4
  • SKIV2L1 2 3
  • SKIV2 3 4
  • 170A 2 3
  • Superkiller Viralicidic Activity 2 (S. Cerevisiae Homolog)-Like 2
  • Superkiller Viralicidic Activity 2-Like (S. Cerevisiae) 2
  • Superkiller Viralicidic Activity 2-Like 3
  • EC 3.6.4.- 4
  • EC 3.6.1 51
  • SKIV2L 5
  • THES2 3
  • SKI2 3
  • Ski2 4
  • 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
  • GC06P031958

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 Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is MTREX.

UniProtKB/Swiss-Prot Summary 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 CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SKIV2L Gene

Genomics for SKIV2L Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SKIV2L Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SKIV2L on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SKIV2L

Top Transcription factor binding sites by QIAGEN in the SKIV2L gene promoter:
  • AP-1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Pax-5
  • RFX1
  • STAT1

Genomic Locations for SKIV2L Gene

Genomic Locations for SKIV2L Gene
chr6:31,959,117-31,969,852
(GRCh38/hg38)
Size:
10,736 bases
Orientation:
Plus strand
chr6:31,926,581-31,937,532
(GRCh37/hg19)
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=Truncated N-terminus.; 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 Lys84, Lys316, Lys363, Lys516, Lys539, Lys720, Lys736, Lys791, Lys837, Lys991, Lys1004, Lys1026, Lys1075, and Lys1225
  • Modification sites at PhosphoSitePlus

Other Protein References for SKIV2L Gene

Antibody Products

  • Boster Bio Antibodies for SKIV2L
  • Santa Cruz Biotechnology (SCBT) Antibodies for SKIV2L

Domains & Families for SKIV2L Gene

Gene Families for SKIV2L Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SKIV2L Gene

Suggested Antigen Peptide Sequences for SKIV2L Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57529, highly similar to Helicase SKI2W (EC 3.6.1.-) (B4DM01_HUMAN)
  • cDNA FLJ61010, highly similar to Helicase SKI2W (EC 3.6.1.-) (B4E0B4_HUMAN)
  • Putative RNA helicase Ski2w (O76046_HUMAN)
  • Superkiller viralicidic activity 2-like (S. cerevisiae), isoform CRA_c (Q5JP73_HUMAN)
  • Superkiller viralicidic activity 2-like (S. cerevisiae) (Q96BC0_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15477

UniProtKB/Swiss-Prot:

SKIV2_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 SKIV2L: view

Function for SKIV2L Gene

Molecular function for SKIV2L Gene

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).
GENATLAS Biochemistry:
superkiller viralicidic activity 2, (S cerevisiae homolog)-like 2,helicase recognized by monoclonal antibody 170A1 with homology to human KIAA052,(superfamily II)

Enzyme Numbers (IUBMB) for SKIV2L Gene

Phenotypes From GWAS Catalog for SKIV2L Gene

Gene Ontology (GO) - Molecular Function for SKIV2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0003724 RNA helicase activity TAS,IBA 21873635
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:
  • Skiv2l Skiv2l<tm2b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for SKIV2L Gene

miRTarBase miRNAs that target SKIV2L

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SKIV2L

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
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SKIV2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0055087 Ski complex IBA,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 IBA 21873635
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay IBA 21873635
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

mRNA/cDNA for SKIV2L Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SKIV2L

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

No ASD Table

Relevant External Links for SKIV2L Gene

GeneLoc Exon Structure 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 and MOPED for SKIV2L Gene



Protein tissue co-expression partners for SKIV2L Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SKIV2L

SOURCE GeneReport for Unigene cluster for SKIV2L Gene:

Hs.89864

Evidence on tissue expression from TISSUES for SKIV2L Gene

  • Liver(4.5)
  • Blood(4.4)
  • Nervous system(2.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SKIV2L Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • lip
  • mouth
  • nose
  • outer ear
  • pharynx
  • salivary gland
  • skull
Thorax:
  • breast
  • esophagus
  • heart
Abdomen:
  • abdominal wall
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
Pelvis:
  • placenta
  • rectum
  • testicle
  • uterus
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • red blood cell
  • skin
  • white blood cell
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 30 31
  • 99.36 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SKIV2L 30 31
  • 90.05 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SKIV2L 30 31
  • 89.7 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SKIV2L 31
  • 88 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Skiv2l 30 17 31
  • 87.53 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Skiv2l 30
  • 87.12 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SKIV2L 31
  • 86 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SKIV2L 31
  • 52 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SKIV2L 31
  • 65 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia skiv2l 30
  • 60.57 (n)
Zebrafish
(Danio rerio)
Actinopterygii skiv2l 30 31
  • 62.54 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003182 30
  • 54.37 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta tst 30 31 32
  • 51.85 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea skih-2 30 31
  • 47.45 (n)
OneToOne
F01G4.3 32
  • 40 (a)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AER067C 30
  • 48.25 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SKI2 30 31 33
  • 47.76 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G46960 30
  • 50.42 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU01857 30
  • 49.99 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC550.03c 30
  • 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for SKIV2L: view image

Paralogs for SKIV2L Gene

Paralogs for SKIV2L Gene

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

  • SKIV2_HUMAN
  • B4E0B4_HUMAN
  • F5H7B0_HUMAN
  • F8WDE8_HUMAN
  • H7C4L3_HUMAN
  • H7C5N0_HUMAN
  • Q96BC0_HUMAN
  • Q9NPK3_HUMAN
genes like me logo Genes that share paralogs with SKIV2L: view

Variants for SKIV2L Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SKIV2L Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
689443 Likely Pathogenic: Trichohepatoenteric syndrome 2 31,968,445(+) T/TA FRAMESHIFT_VARIANT
770172 Benign: Trichohepatoenteric syndrome 2; not provided 31,961,338(+) C/G MISSENSE_VARIANT
800925 Pathogenic: Trichohepatoenteric syndrome 2 31,969,532(+) AGGGCTCTCAGGGACC INFRAME_DELETION
817878 Pathogenic: not provided 31,963,962(+) AG/A FRAMESHIFT_VARIANT
828128 Likely Pathogenic: Trichohepatoenteric syndrome 2 31,962,985(+) C/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SKIV2L Gene

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

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

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)

Additional Variant Information 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

(14) MalaCards diseases for SKIV2L Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- 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.

Additional Disease Information for SKIV2L

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 SG … Song K (Genomics 1995) 2 3 4 23
  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 23 41
  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 CY (Genomics 1998) 2 3 23
  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 AW … Yu CY (Nucleic acids research 1995) 3 4 23
  5. SKIV2L mutations cause syndromic diarrhea, or trichohepatoenteric syndrome. (PMID: 22444670) Fabre A … Badens C (American journal of human genetics 2012) 3 4

Products for SKIV2L Gene

Sources for SKIV2L Gene