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Aliases for RTRAF Gene

Aliases for RTRAF Gene

  • RNA Transcription, Translation And Transport Factor 2 3
  • C14orf166 3 4 5
  • Chromosome 14 Open Reading Frame 166 2 5
  • RLL Motif Containing 1 2 3
  • CLE7 Homolog 3 4
  • CLE 3 4
  • UPF0568 Protein C14orf166 3
  • LCRP369 3
  • CGI-99 3
  • CGI99 3
  • RLLM1 3
  • HCLE1 3
  • CLE7 3

External Ids for RTRAF Gene

Previous HGNC Symbols for RTRAF Gene

  • C14orf166

Summaries for RTRAF Gene

GeneCards Summary for RTRAF Gene

RTRAF (RNA Transcription, Translation And Transport Factor) is a Protein Coding gene. Diseases associated with RTRAF include Influenza and Leukoencephalopathy With Vanishing White Matter. Among its related pathways are Gene Expression and tRNA processing.

UniProtKB/Swiss-Prot for RTRAF Gene

  • RNA-binding protein involved in modulation of mRNA transcription by Polymerase II. In case of infection by influenza virus A, is involved in viral replication. Component of the tRNA-splicing ligase complex and is required for tRNA ligation (PubMed:24870230). May be required for RNA transport (PubMed:24608264).

Gene Wiki entry for RTRAF Gene

Additional gene information for RTRAF Gene

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

Genomics for RTRAF Gene

Regulatory Elements for RTRAF Gene

Enhancers for RTRAF 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
GH14H051988 1.3 ENCODE dbSUPER 17.6 +0.1 141 2 PKNOX1 SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 FOS SP3 ZHX2 RTRAF GNG2 LOC105370500 GC14M051998
GH14H051843 1.7 FANTOM5 Ensembl ENCODE dbSUPER 12 -142.6 -142644 5 HDGF PKNOX1 TBL1XR1 SIN3A BMI1 BATF RFX5 ELK1 ZNF143 ZNF207 GNG2 RTRAF PTGDR PTGER2 LOC102723604
GH14H051871 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -116.5 -116492 2 TBL1XR1 BMI1 BATF ZNF366 SCRT2 FOS ATF7 ETV6 RUNX3 CREM GNG2 RTRAF PTGER2 PTGDR LOC102723604
GH14H051884 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.5 -105.0 -104995 1 HDAC1 RB1 MAX POLR2A ATF7 RCOR1 ETV6 RUNX3 IKZF2 RNF2 GNG2 RTRAF PTGER2 LOC102723604
GH14H051859 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.4 -127.0 -127000 5 HDGF PKNOX1 RB1 RAD21 ZNF366 ATF7 ETV6 RUNX3 CREM IKZF2 GNG2 RTRAF PTGER2 LOC102723604
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTRAF on UCSC Golden Path with GeneCards custom track

Promoters for RTRAF Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000068362 325 1601 PKNOX1 SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 FOS SP3 ZHX2

Genomic Location for RTRAF Gene

Chromosome:
14
Start:
51,989,475 bp from pter
End:
52,010,691 bp from pter
Size:
21,217 bases
Orientation:
Plus strand

Genomic View for RTRAF Gene

Genes around RTRAF on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RTRAF Gene

Proteins for RTRAF Gene

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

    Protein Symbol:
    Q9Y224-CN166_HUMAN
    Recommended name:
    UPF0568 protein C14orf166
    Protein Accession:
    Q9Y224

    Protein attributes for RTRAF Gene

    Size:
    244 amino acids
    Molecular mass:
    28068 Da
    Quaternary structure:
    • Homodimer (Probable). Interacts with NIN; which may prevent phosphorylation of NIN. Interacts with POLR2A. Component of a tRNA-splicing ligase complex with FAM98B, DDX1 and RTCB. Interacts with influenza A virus RNA polymerase subunits PA, PB1 and PB2, and nucleocapsid NP. Interacts with hepatitis C virus core protein p19.

neXtProt entry for RTRAF Gene

Post-translational modifications for RTRAF Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RTRAF Gene

No data available for DME Specific Peptides for RTRAF Gene

Domains & Families for RTRAF Gene

Gene Families for RTRAF Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RTRAF Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RTRAF Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y224

UniProtKB/Swiss-Prot:

CN166_HUMAN :
  • Belongs to the UPF0568 family.
Family:
  • Belongs to the UPF0568 family.
genes like me logo Genes that share domains with RTRAF: view

Function for RTRAF Gene

Molecular function for RTRAF Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein involved in modulation of mRNA transcription by Polymerase II. In case of infection by influenza virus A, is involved in viral replication. Component of the tRNA-splicing ligase complex and is required for tRNA ligation (PubMed:24870230). May be required for RNA transport (PubMed:24608264).

Phenotypes From GWAS Catalog for RTRAF Gene

Gene Ontology (GO) - Molecular Function for RTRAF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II core binding IDA 16950395
GO:0003723 RNA binding IEA,IDA 22658674
GO:0005515 protein binding IPI 11507205
GO:0042802 identical protein binding IPI 15147888
genes like me logo Genes that share ontologies with RTRAF: view
genes like me logo Genes that share phenotypes with RTRAF: view

Animal Models for RTRAF Gene

MGI Knock Outs for RTRAF:

Animal Model Products

CRISPR Products

miRNA for RTRAF Gene

miRTarBase miRNAs that target RTRAF

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RTRAF
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RTRAF Gene

Localization for RTRAF Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTRAF Gene

Nucleus. Cytoplasm, cytosol. Cytoplasm, perinuclear region. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=May localize at the centrosome during mitosis. Shuttles between the cytosol and the nucleus: enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low (PubMed:24608264). {ECO:0000269 PubMed:24608264}.

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 RTRAF gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RTRAF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 24608264
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA,IDA 24608264
GO:0005815 microtubule organizing center IEA --
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with RTRAF: view

Pathways & Interactions for RTRAF Gene

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

Pathways by source for RTRAF Gene

Gene Ontology (GO) - Biological Process for RTRAF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS --
GO:0016032 viral process IEA --
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IMP 16950395
genes like me logo Genes that share ontologies with RTRAF: view

No data available for SIGNOR curated interactions for RTRAF Gene

Drugs & Compounds for RTRAF Gene

No Compound Related Data Available

Transcripts for RTRAF Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RTRAF
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for RTRAF Gene

GeneLoc Exon Structure for
RTRAF
ECgene alternative splicing isoforms for
RTRAF

Expression for RTRAF Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of RTRAF Gene:

RTRAF

mRNA Expression by UniProt/SwissProt for RTRAF Gene:

Q9Y224-CN166_HUMAN
Tissue specificity: Widely expressed. Expressed at high level in heart and skeletal muscle. Expressed at intermediate level in liver, pancreas, fetal brain and fetal lung. Weakly expressed in adult brain, adult lung, placenta, fetal liver and fetal kidney. Overexpressed in many brain tumors.

Evidence on tissue expression from TISSUES for RTRAF Gene

  • Nervous system(4.6)
  • Liver(4.5)
  • Muscle(4.5)
  • Lung(3.1)
  • Pancreas(2.7)
  • Heart(2.6)
  • Lymph node(2.5)
  • Spleen(2.3)
  • Kidney(2.2)
  • Intestine(2)
genes like me logo Genes that share expression patterns with RTRAF: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RTRAF Gene

Orthologs for RTRAF Gene

This gene was present in the common ancestor of animals.

Orthologs for RTRAF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C14ORF166 34
  • 100 (a)
OneToOne
C14H14orf166 33
  • 99.73 (n)
dog
(Canis familiaris)
Mammalia C14orf166 34
  • 99 (a)
OneToOne
C8H14orf166 33
  • 94.54 (n)
cow
(Bos Taurus)
Mammalia C10H14ORF166 34
  • 98 (a)
OneToOne
C10H14orf166 33
  • 94.13 (n)
mouse
(Mus musculus)
Mammalia Gm10704 34
  • 95 (a)
OneToMany
2700060E02Rik 33 16 34
  • 92.35 (n)
oppossum
(Monodelphis domestica)
Mammalia C14orf166 34
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia RGD1304704 33
  • 89.62 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia C14orf166 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves C5H14ORF166 34 33
  • 83.68 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C14orf166 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493394 33
  • 76.25 (n)
Str.9974 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.18755 33
zebrafish
(Danio rerio)
Actinopterygii C17H14orf166 34
  • 85 (a)
OneToOne
zgc:56576 33
  • 73.28 (n)
zgc56576 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6642 33
fruit fly
(Drosophila melanogaster)
Insecta CG31249 33 34
  • 50.23 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001816 33
  • 49.52 (n)
worm
(Caenorhabditis elegans)
Secernentea E02H1.5 34
  • 23 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3718 33
Species where no ortholog for RTRAF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RTRAF Gene

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

Paralogs for RTRAF Gene

Pseudogenes.org Pseudogenes for RTRAF Gene

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

No data available for Paralogs for RTRAF Gene

Variants for RTRAF Gene

Sequence variations from dbSNP and Humsavar for RTRAF Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs1000041219 -- 51,990,812(+) TTTAC(-/TTA)TTATT intron-variant
rs1000056572 -- 51,992,827(+) GGGGT(C/T)CGAGA intron-variant
rs1000173336 -- 52,005,175(+) AATTC(G/T)TAGTT intron-variant, utr-variant-3-prime
rs1000213083 -- 52,004,845(+) GAAAA(C/T)TTTAA intron-variant, utr-variant-3-prime
rs1000237193 -- 51,996,727(+) AACCA(A/C)AGTAC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv952842 CNV duplication 24416366

Variation tolerance for RTRAF Gene

Residual Variation Intolerance Score: 48.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 15.99% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTRAF Gene

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

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

Disorders for RTRAF Gene

MalaCards: The human disease database

(2) MalaCards diseases for RTRAF Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
influenza
  • flu
leukoencephalopathy with vanishing white matter
  • ovarioleukodystrophy
- elite association - COSMIC cancer census association via MalaCards
Search RTRAF in MalaCards View complete list of genes associated with diseases

Relevant External Links for RTRAF

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTRAF
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTRAF
genes like me logo Genes that share disorders with RTRAF: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RTRAF Gene

Publications for RTRAF Gene

  1. hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. (PMID: 24608264) Pérez-González A … Nieto A (PloS one 2014) 2 3 4 60
  2. A novel ninein-interaction protein, CGI-99, blocks ninein phosphorylation by GSK3beta and is highly expressed in brain tumors. (PMID: 15147888) Howng SL … Hong YR (FEBS letters 2004) 3 4 22 60
  3. PA subunit from influenza virus polymerase complex interacts with a cellular protein with homology to a family of transcriptional activators. (PMID: 11507205) Huarte M … Nieto A (Journal of virology 2001) 2 3 4 60
  4. hCLE/C14orf166, a cellular protein required for viral replication, is incorporated into influenza virus particles. (PMID: 26864902) Rodriguez-Frandsen A … Nieto A (Scientific reports 2016) 2 3 60
  5. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. (PMID: 24870230) Popow J … Martinez J (Nature 2014) 3 4 60

Products for RTRAF Gene

Sources for RTRAF Gene

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