RNF138 Gene (Protein Coding)

Ring Finger Protein 138

GC18P032091
GIFtS:
41
The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-DNA and protein-protein interactions. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008] See more...

Aliases for RNF138 Gene

Aliases for RNF138 Gene

  • Ring Finger Protein 138 2 3 5
  • NARF 2 3 4
  • Ring Finger Protein 138, E3 Ubiquitin Protein Ligase 2 3
  • Nemo-Like Kinase Associated Ring Finger Protein 2 3
  • Nemo-Like Kinase-Associated RING Finger Protein 3 4
  • RING-Type E3 Ubiquitin Transferase RNF138 3 4
  • E3 Ubiquitin-Protein Ligase RNF138 3 4
  • NLK-Associated RING Finger Protein 3 4
  • STRIN 2 3
  • HNARF 3 4
  • Testicular Tissue Protein Li 165 3
  • RING Finger Protein 138 4
  • EC 2.3.2.27 4
  • RNF138 5
  • HSD-4 3

External Ids for RNF138 Gene

Previous GeneCards Identifiers for RNF138 Gene

  • GC18P029559
  • GC18P027924
  • GC18P027923
  • GC18P027925
  • GC18P029671
  • GC18P026528

Summaries for RNF138 Gene

Entrez Gene Summary for RNF138 Gene

  • The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-DNA and protein-protein interactions. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

GeneCards Summary for RNF138 Gene

RNF138 (Ring Finger Protein 138) is a Protein Coding gene. Diseases associated with RNF138 include Episodic Ataxia, Type 2 and Episodic Ataxia. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include protein kinase binding and ligase activity. An important paralog of this gene is RNF166.

UniProtKB/Swiss-Prot Summary for RNF138 Gene

  • E3 ubiquitin-protein ligase involved in DNA damage response by promoting DNA resection and homologous recombination (PubMed:26502055, PubMed:26502057). Recruited to sites of double-strand breaks following DNA damage and specifically promotes double-strand break repair via homologous recombination (PubMed:26502055, PubMed:26502057). Two different, non-exclusive, mechanisms have been proposed. According to a report, regulates the choice of double-strand break repair by favoring homologous recombination over non-homologous end joining (NHEJ): acts by mediating ubiquitination of XRCC5/Ku80, leading to remove the Ku complex from DNA breaks, thereby promoting homologous recombination (PubMed:26502055). According to another report, cooperates with UBE2Ds E2 ubiquitin ligases (UBE2D1, UBE2D2, UBE2D3 or UBE2D4) to promote homologous recombination by mediating ubiquitination of RBBP8/CtIP (PubMed:26502057). Together with NLK, involved in the ubiquitination and degradation of TCF/LEF (PubMed:16714285). Also exhibits auto-ubiquitination activity in combination with UBE2K (PubMed:16714285). May act as a negative regulator in the Wnt/beta-catenin-mediated signaling pathway (PubMed:16714285).

Additional gene information for RNF138 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RNF138 Gene

Genomics for RNF138 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RNF138 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 RNF138 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RNF138

Top Transcription factor binding sites by QIAGEN in the RNF138 gene promoter:
  • c-Myc
  • CUTL1
  • HFH-1
  • Max
  • STAT5B

Genomic Locations for RNF138 Gene

Latest Assembly
chr18:32,091,858-32,131,561
(GRCh38/hg38)
Size:
39,704 bases
Orientation:
Plus strand

Previous Assembly
chr18:29,671,837-29,711,524
(GRCh37/hg19 by Entrez Gene)
Size:
39,688 bases
Orientation:
Plus strand

chr18:29,671,818-29,711,524
(GRCh37/hg19 by Ensembl)
Size:
39,707 bases
Orientation:
Plus strand

Genomic View for RNF138 Gene

Genes around RNF138 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF138 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF138 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RNF138 Gene

Proteins for RNF138 Gene

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  • Protein details for RNF138 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WVD3-RN138_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF138
    Protein Accession:
    Q8WVD3
    Secondary Accessions:
    • B2RE17
    • Q9H8K2
    • Q9UF87
    • Q9UKI6

    Protein attributes for RNF138 Gene

    Size:
    245 amino acids
    Molecular mass:
    28193 Da
    Quaternary structure:
    • Interacts with NLK (PubMed:16714285). Interacts with XRCC5/Ku80 (PubMed:26502055). Interacts with RBBP8/CtIP (PubMed:26502057).

    Alternative splice isoforms for RNF138 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF138 Gene

Protein Expression for RNF138 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RNF138 Gene

  • Auto-ubiquitinated.
  • Ubiquitination at Lys26, Lys41, Lys158, Lys91, and Lys94
  • Modification sites at PhosphoSitePlus

Other Protein References for RNF138 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RNF138 Gene

Domains & Families for RNF138 Gene

Gene Families for RNF138 Gene

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

Protein Domains for RNF138 Gene

InterPro:
Blocks:
  • Zn-finger, RING
ProtoNet:

Suggested Antigen Peptide Sequences for RNF138 Gene

GenScript: Design optimal peptide antigens:
  • RING finger protein 138 (RN138_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WVD3

UniProtKB/Swiss-Prot:

RN138_HUMAN :
  • The zinc finger domains (C2H2-type and C2HC-type zinc fingers) bind DNA and mediate recruitment to double-strand break sites. They show strong preference for DNA with 5'- or 3'-single-stranded overhangs, while they do not bind blunt-ended double-stranded DNA or poly(ADP-ribose) (PAR) polymers.
Domain:
  • The zinc finger domains (C2H2-type and C2HC-type zinc fingers) bind DNA and mediate recruitment to double-strand break sites. They show strong preference for DNA with 5'- or 3'-single-stranded overhangs, while they do not bind blunt-ended double-stranded DNA or poly(ADP-ribose) (PAR) polymers.
genes like me logo Genes that share domains with RNF138: view

Function for RNF138 Gene

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Molecular function for RNF138 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase involved in DNA damage response by promoting DNA resection and homologous recombination (PubMed:26502055, PubMed:26502057). Recruited to sites of double-strand breaks following DNA damage and specifically promotes double-strand break repair via homologous recombination (PubMed:26502055, PubMed:26502057). Two different, non-exclusive, mechanisms have been proposed. According to a report, regulates the choice of double-strand break repair by favoring homologous recombination over non-homologous end joining (NHEJ): acts by mediating ubiquitination of XRCC5/Ku80, leading to remove the Ku complex from DNA breaks, thereby promoting homologous recombination (PubMed:26502055). According to another report, cooperates with UBE2Ds E2 ubiquitin ligases (UBE2D1, UBE2D2, UBE2D3 or UBE2D4) to promote homologous recombination by mediating ubiquitination of RBBP8/CtIP (PubMed:26502057). Together with NLK, involved in the ubiquitination and degradation of TCF/LEF (PubMed:16714285). Also exhibits auto-ubiquitination activity in combination with UBE2K (PubMed:16714285). May act as a negative regulator in the Wnt/beta-catenin-mediated signaling pathway (PubMed:16714285).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27; Evidence={ECO:0000305};.

Enzyme Numbers (IUBMB) for RNF138 Gene

Gene Ontology (GO) - Molecular Function for RNF138 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003697 single-stranded DNA binding IBA,IDA 26502055
GO:0005515 protein binding IPI 19549727
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with RNF138: view
genes like me logo Genes that share phenotypes with RNF138: view

Animal Models for RNF138 Gene

MGI Knock Outs for RNF138:
  • Rnf138 Rnf138<tm1b(EUCOMM)Hmgu>

Animal Models for research

Inhibitory RNAs for research

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No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RNF138 Gene

Localization for RNF138 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF138 Gene

Chromosome. Note=Recruited at DNA damage sites (PubMed:26502055). Localizes to sites of double-strand break: localization to double-strand break sites is mediated by the zinc fingers (PubMed:26502055, PubMed:26502057). {ECO:0000269 PubMed:26502055, ECO:0000269 PubMed:26502057}.

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 RNF138 gene
Compartment Confidence
nucleus 5
extracellular 2
mitochondrion 2
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RNF138 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA 21630459
GO:0005694 chromosome IEA --
GO:0035861 site of double-strand break IBA,IDA 26502055
genes like me logo Genes that share ontologies with RNF138: view

Pathways & Interactions for RNF138 Gene

genes like me logo Genes that share pathways with RNF138: view

UniProtKB/Swiss-Prot Q8WVD3-RN138_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RNF138 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IBA,IMP 26502055
GO:0006281 DNA repair IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0010792 DNA double-strand break processing involved in repair via single-strand annealing IBA,IMP 26502057
GO:0016055 Wnt signaling pathway IEA --
genes like me logo Genes that share ontologies with RNF138: view

No data available for SIGNOR curated interactions for RNF138 Gene

Drugs & Compounds for RNF138 Gene

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(3) Drugs for RNF138 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine monophosphate Approved, Investigational Nutra 0
Phosphate Experimental Pharma 0
ATP Investigational Nutra 0

(1) Additional Compounds for RNF138 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(HO)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • Pyrophosphoric acid
 14000-31-8
genes like me logo Genes that share compounds with RNF138: view

Transcripts for RNF138 Gene

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mRNA/cDNA for RNF138 Gene

3 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RNF138

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Alternative Splicing Database (ASD) splice patterns (SP) for RNF138 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9
SP1: - -
SP2:
SP3: - - -
SP4: - - -
SP5: -
SP6: -

Relevant External Links for RNF138 Gene

GeneLoc Exon Structure for
RNF138

Expression for RNF138 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RNF138 Gene

mRNA expression in normal human tissues for RNF138 Gene
mRNA expression by GTEx for RNF138 GenemRNA expression by BioGPS for RNF138 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RNF138 Gene

This gene is overexpressed in Testis (x5.8).

Protein differential expression in normal tissues from HIPED for RNF138 Gene

This gene is overexpressed in Lung (37.9), Fetal ovary (14.0), and Testis (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RNF138 Gene



Protein tissue co-expression partners for RNF138 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RNF138

SOURCE GeneReport for Unigene cluster for RNF138 Gene:

Hs.302408

Evidence on tissue expression from TISSUES for RNF138 Gene

  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with RNF138: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF138 Gene

Orthologs for RNF138 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNF138 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RNF138 30 31
  • 99.86 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RNF138 30 31
  • 96.14 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RNF138 30 31
  • 95.24 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Rnf138 30 17 31
  • 93.33 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rnf138 30
  • 90.59 (n)
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 88 (a)
 OneToMany
-- 31
  • 86 (a)
 OneToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia RNF138 31
  • 88 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves RNF138 30 31
  • 75.96 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RNF138 31
  • 58 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rnf138 30
  • 60.94 (n)
Species where no ortholog for RNF138 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for RNF138 Gene

ENSEMBL:
Gene Tree for RNF138 (if available)
TreeFam:
Gene Tree for RNF138 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RNF138: view image

Paralogs for RNF138 Gene

Paralogs for RNF138 Gene

(6) SIMAP similar genes for RNF138 Gene using alignment to 5 proteins:

  • RN138_HUMAN
  • J3KRU4_HUMAN
  • J3KSI2_HUMAN
  • J3QKM8_HUMAN
  • J3QLQ3_HUMAN

Pseudogenes.org Pseudogenes for RNF138 Gene

genes like me logo Genes that share paralogs with RNF138: view

Variants for RNF138 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RNF138 Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
rs7229690 - p.Lys81Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RNF138 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RNF138 Gene

Variant ID Type Subtype PubMed ID
esv2141547 CNV deletion 18987734
esv2716941 CNV deletion 23290073
esv2716942 CNV deletion 23290073
esv2716943 CNV deletion 23290073
esv2716944 CNV deletion 23290073
esv2758719 CNV gain 17122850
esv3642144 CNV gain 21293372
esv3642146 CNV gain 21293372
nsv1055457 CNV gain 25217958
nsv2248 CNV insertion 18451855
nsv962874 CNV duplication 23825009

Variation tolerance for RNF138 Gene

Residual Variation Intolerance Score: 58.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.54; 44.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF138 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF138

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF138 Gene

Disorders for RNF138 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RNF138 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
episodic ataxia, type 2
  • ea2
episodic ataxia
  • isaacs syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RNF138

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RNF138: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RNF138 Gene

Publications for RNF138 Gene

  1. NARF, an nemo-like kinase (NLK)-associated ring finger protein regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF). (PMID: 16714285) Yamada M … Shibuya H (The Journal of biological chemistry 2006) 2 3 4
  2. Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair. (PMID: 26502057) Schmidt CK … Jackson SP (Nature cell biology 2015) 3 4
  3. The RNF138 E3 ligase displaces Ku to promote DNA end resection and regulate DNA repair pathway choice. (PMID: 26502055) Ismail IH … Hendzel MJ (Nature cell biology 2015) 3 4
  4. A novel gene RNF138 expressed in human gliomas and its function in the glioma cell line U251. (PMID: 22155992) Zhou YX … Du ZW (Analytical cellular pathology (Amsterdam) 2012) 2 3
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41

ExternalLinks

View latest publications for RNF138 gene in Mastermind

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