The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. The specific function of this gene has not yet been determined. Alternatively spliced transcript variants that encode the same protein have been reported. A pseudogene, which is also located on chromosome 3, has been defined for this gene. [provided by Ref... See more...

Aliases for RNF13 Gene

Aliases for RNF13 Gene

  • Ring Finger Protein 13 2 3 5
  • RING-Type E3 Ubiquitin Transferase RNF13 3 4
  • E3 Ubiquitin-Protein Ligase RNF13 3 4
  • RZF 3 4
  • RING Zinc Finger Protein 3
  • RING Finger Protein 13 4
  • EC 2.3.2.27 4
  • EIEE73 3

External Ids for RNF13 Gene

Previous GeneCards Identifiers for RNF13 Gene

  • GC03P146460
  • GC03P150415
  • GC03P150812
  • GC03P150851
  • GC03P151013
  • GC03P149531
  • GC03P146902

Summaries for RNF13 Gene

Entrez Gene Summary for RNF13 Gene

  • The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. The specific function of this gene has not yet been determined. Alternatively spliced transcript variants that encode the same protein have been reported. A pseudogene, which is also located on chromosome 3, has been defined for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for RNF13 Gene

RNF13 (Ring Finger Protein 13) is a Protein Coding gene. Diseases associated with RNF13 include Epileptic Encephalopathy, Early Infantile, 73 and Eccrine Porocarcinoma. Gene Ontology (GO) annotations related to this gene include ligase activity and ubiquitin-protein transferase activity. An important paralog of this gene is RNF167.

UniProtKB/Swiss-Prot Summary for RNF13 Gene

  • E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation. Involved in apoptosis regulation. Mediates ER stress-induced activation of JNK signaling pathway and apoptosis by promoting ERN1 activation and splicing of XBP1 mRNA (PubMed:23378536, PubMed:30595371).

Gene Wiki entry for RNF13 Gene

Additional gene information for RNF13 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RNF13 Gene

Genomics for RNF13 Gene

GeneHancer (GH) Regulatory Elements for RNF13 Gene

Promoters and enhancers for RNF13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J149811 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 523.4 +2.7 2717 6.8 FOXK2 ZBTB40 ZNF217 SIN3A TCF12 USF1 POLR2G SP1 RBAK PHF8 RNF13 PFN2 ENSG00000242791 COMMD2 lnc-RNF13-4 piR-38051-192 ANKUB1 lnc-ANKUB1-2
GH03J149809 Enhancer 0.5 FANTOM5 19.4 -2.5 -2519 0.3 ATF2 PRDM6 ZNF18 ATF7 RF00017-4138 RNF13 lnc-COMMD2-3 lnc-RNF13-4 ANKUB1 lnc-ANKUB1-2
GH03J149782 Enhancer 0.6 ENCODE 12.9 -28.8 -28792 2.3 USF1 JUND FOS FOSL2 CEBPB JUN BATF GATA3 JUNB IKZF1 RNF13 WWTR1 WWTR1-AS1 ENSG00000242791 piR-41306-193 lnc-COMMD2-3 lnc-RNF13-4 ANKUB1 lnc-ANKUB1-2
GH03J149848 Enhancer 0.5 FANTOM5 Ensembl 15.2 +36.6 36617 3.8 SPI1 RNF13 ENSG00000242791 PFN2 piR-38051-192 lnc-RNF13-4 lnc-ANKUB1-2 ANKUB1
GH03J149462 Enhancer 0.7 FANTOM5 Ensembl dbSUPER 9.4 -349.6 -349583 1 HLF ENSG00000241929 FKBP1AP4 TM4SF1 TM4SF1-AS1 RNF13 piR-42700-091
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNF13 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RNF13

Top Transcription factor binding sites by QIAGEN in the RNF13 gene promoter:
  • Lhx3a
  • LHX3b
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • POU2F1
  • POU2F1a

Genomic Locations for RNF13 Gene

Genomic Locations for RNF13 Gene
chr3:149,812,484-149,962,139
(GRCh38/hg38)
Size:
149,656 bases
Orientation:
Plus strand
chr3:149,530,475-149,679,926
(GRCh37/hg19)
Size:
149,452 bases
Orientation:
Plus strand

Genomic View for RNF13 Gene

Genes around RNF13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF13 Gene

Proteins for RNF13 Gene

  • Protein details for RNF13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43567-RNF13_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF13
    Protein Accession:
    O43567
    Secondary Accessions:
    • A6NC87
    • B3KR12
    • Q05D66
    • Q6IBJ9

    Protein attributes for RNF13 Gene

    Size:
    381 amino acids
    Molecular mass:
    42814 Da
    Quaternary structure:
    • Interacts with ERN1.
    SequenceCaution:
    • Sequence=AAH17878.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RNF13 Gene

    Alternative splice isoforms for RNF13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF13 Gene

Post-translational modifications for RNF13 Gene

No data available for DME Specific Peptides for RNF13 Gene

Domains & Families for RNF13 Gene

Gene Families for RNF13 Gene

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

Protein Domains for RNF13 Gene

Blocks:
  • Zn-finger, RING
  • Protease-associated PA
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RNF13 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ33452 fis, clone BRAMY2000151, highly similar to RING finger protein 13 (B3KR12_HUMAN)
  • RNF13 protein (Q05D66_HUMAN)
  • RING finger protein 13 (RNF13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43567

UniProtKB/Swiss-Prot:

RNF13_HUMAN :
  • The RING-type zinc finger domain is required for E3 ligase activity and for promoting ER stress-induced JNK activation and apoptosis.
Domain:
  • The RING-type zinc finger domain is required for E3 ligase activity and for promoting ER stress-induced JNK activation and apoptosis.
genes like me logo Genes that share domains with RNF13: view

Function for RNF13 Gene

Molecular function for RNF13 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation. Involved in apoptosis regulation. Mediates ER stress-induced activation of JNK signaling pathway and apoptosis by promoting ERN1 activation and splicing of XBP1 mRNA (PubMed:23378536, PubMed:30595371).
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;.

Enzyme Numbers (IUBMB) for RNF13 Gene

Phenotypes From GWAS Catalog for RNF13 Gene

Gene Ontology (GO) - Molecular Function for RNF13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity ISS --
GO:0005515 protein binding IPI 19690564
GO:0008432 JUN kinase binding IDA 23378536
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RNF13: view
genes like me logo Genes that share phenotypes with RNF13: view

Human Phenotype Ontology for RNF13 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RNF13 Gene

MGI Knock Outs for RNF13:
  • Rnf13 Rnf13<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for RNF13 Gene

Localization for RNF13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF13 Gene

Endoplasmic reticulum membrane. Golgi apparatus membrane. Late endosome membrane; Single-pass membrane protein. Lysosome membrane. Nucleus inner membrane. Note=Under certain conditions, relocalizes to recycling endosomes and to the inner nuclear membrane. {ECO:0000250}.

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 RNF13 gene
Compartment Confidence
endoplasmic reticulum 5
nucleus 4
endosome 4
cytosol 4
plasma membrane 3
golgi apparatus 3
extracellular 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (3)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RNF13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005634 nucleus IEA --
GO:0005637 nuclear inner membrane IEA --
GO:0005654 nucleoplasm IDA --
GO:0005764 lysosome IEA --
genes like me logo Genes that share ontologies with RNF13: view

Pathways & Interactions for RNF13 Gene

PathCards logo

SuperPathways for RNF13 Gene

No Data Available

UniProtKB/Swiss-Prot O43567-RNF13_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RNF13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process IBA 21873635
GO:0016567 protein ubiquitination IEA --
GO:0051865 protein autoubiquitination ISS --
GO:0070304 positive regulation of stress-activated protein kinase signaling cascade IMP 23378536
genes like me logo Genes that share ontologies with RNF13: view

No data available for Pathways by source and SIGNOR curated interactions for RNF13 Gene

Drugs & Compounds for RNF13 Gene

(1) Drugs for RNF13 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with RNF13: view

Transcripts for RNF13 Gene

mRNA/cDNA for RNF13 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNF13 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1:
SP2: - - -
SP3: - - -
SP4:

Relevant External Links for RNF13 Gene

GeneLoc Exon Structure for
RNF13

Expression for RNF13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RNF13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RNF13 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.2).

Protein differential expression in normal tissues from HIPED for RNF13 Gene

This gene is overexpressed in Heart (33.5), Peripheral blood mononuclear cells (9.8), Skin (8.3), and Testis (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RNF13 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RNF13

SOURCE GeneReport for Unigene cluster for RNF13 Gene:

Hs.12333

mRNA Expression by UniProt/SwissProt for RNF13 Gene:

O43567-RNF13_HUMAN
Tissue specificity: Widely expressed (at protein level). In normal pancreas, expressed in islets, but not in ducts, nor in acini (at protein level).

Evidence on tissue expression from TISSUES for RNF13 Gene

  • Nervous system(4.9)
  • Muscle(4.3)
  • Spleen(4.3)
  • Lung(2.7)
genes like me logo Genes that share expression patterns with RNF13: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF13 Gene

Orthologs for RNF13 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RNF13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RNF13 31 30
  • 100 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RNF13 31 30
  • 95.61 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RNF13 31 30
  • 92.83 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RNF13 31
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNF13 31
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf13 17 31 30
  • 89.59 (n)
chicken
(Gallus gallus)
Aves RNF13 31 30
  • 80.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RNF13 31
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf13 30
  • 70.95 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68556 30
zebrafish
(Danio rerio)
Actinopterygii rnf13 30
  • 68.98 (n)
zgc55660 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002028 30
  • 45.56 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10277 31 32
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea C18B12.4 31
  • 22 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons RMR1 30
  • 47.84 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.598 31
  • 32 (a)
OneToMany
Cin.7712 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7712 30
Species where no ortholog for RNF13 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 RNF13 Gene

ENSEMBL:
Gene Tree for RNF13 (if available)
TreeFam:
Gene Tree for RNF13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RNF13: view image

Paralogs for RNF13 Gene

Paralogs for RNF13 Gene

(6) SIMAP similar genes for RNF13 Gene using alignment to 15 proteins:

  • RNF13_HUMAN
  • B3KR12_HUMAN
  • C9IY58_HUMAN
  • C9J383_HUMAN
  • C9J7B4_HUMAN
  • C9J8T4_HUMAN
  • C9JCY0_HUMAN
  • C9JRV0_HUMAN
  • C9JU37_HUMAN
  • C9JYN7_HUMAN
  • C9JYY4_HUMAN
  • F8WDJ5_HUMAN
  • F8WEX6_HUMAN
  • H7C5Q6_HUMAN
  • Q05D66_HUMAN

Pseudogenes.org Pseudogenes for RNF13 Gene

genes like me logo Genes that share paralogs with RNF13: view

Variants for RNF13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RNF13 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
775913 Benign: not provided 149,911,994(+) G/A MISSENSE_VARIANT
782436 Benign: not provided 149,960,048(+) G/C INTRON_VARIANT
rs1559980771 Pathogenic: EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 73 149,960,890(+) T/C MISSENSE_VARIANT
rs1559980785 Pathogenic: EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 73 149,960,893(+) T/C MISSENSE_VARIANT
VAR_082117 Epileptic encephalopathy, early infantile, 73 (EIEE73) [MIM:618379] p.Leu311Ser

Additional dbSNP identifiers (rs#s) for RNF13 Gene

Structural Variations from Database of Genomic Variants (DGV) for RNF13 Gene

Variant ID Type Subtype PubMed ID
esv1516102 CNV insertion 17803354
esv2597752 CNV deletion 19546169
esv2664861 CNV deletion 23128226
esv2676965 CNV deletion 23128226
esv3353996 CNV insertion 20981092
esv34142 CNV loss 18971310
esv3562714 CNV deletion 23714750
esv3598149 CNV loss 21293372
esv3598150 CNV loss 21293372
esv3598151 CNV loss 21293372
esv993688 CNV insertion 20482838
nsv1110769 CNV insertion 24896259
nsv1125783 CNV tandem duplication 24896259
nsv965222 CNV duplication 23825009

Variation tolerance for RNF13 Gene

Residual Variation Intolerance Score: 49.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.93; 49.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF13

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF13 Gene

Disorders for RNF13 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RNF13 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 73
  • eiee73
eccrine porocarcinoma
  • eccrine porocarcinoma of skin
prader-willi syndrome
  • pws
- elite association - COSMIC cancer census association via MalaCards
Search RNF13 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RNF13_HUMAN
  • Epileptic encephalopathy, early infantile, 73 (EIEE73) [MIM:618379]: A form of epileptic encephalopathy, a heterogeneous group of severe early-onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE73 is an autosomal dominant form with onset at birth. {ECO:0000269 PubMed:30595371}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RNF13

genes like me logo Genes that share disorders with RNF13: view

No data available for Genatlas for RNF13 Gene

Publications for RNF13 Gene

  1. Heterozygous RNF13 Gain-of-Function Variants Are Associated with Congenital Microcephaly, Epileptic Encephalopathy, Blindness, and Failure to Thrive. (PMID: 30595371) Edvardson S … Moldovan GL (American journal of human genetics 2019) 3 4 54
  2. RNF13, a RING finger protein, mediates endoplasmic reticulum stress-induced apoptosis through the inositol-requiring enzyme (IRE1α)/c-Jun NH2-terminal kinase pathway. (PMID: 23378536) Arshad M … Li P (The Journal of biological chemistry 2013) 3 4 54
  3. Nuclear targeting of an endosomal E3 ubiquitin ligase. (PMID: 20230530) Bocock JP … Erickson AH (Traffic (Copenhagen, Denmark) 2010) 3 23 54
  4. RNF13: a novel RING-type ubiquitin ligase over-expressed in pancreatic cancer. (PMID: 18794910) Zhang Q … Zhu D (Cell research 2009) 3 4 54
  5. Integral and associated lysosomal membrane proteins. (PMID: 17897319) Schröder B … Hasilik A (Traffic (Copenhagen, Denmark) 2007) 3 4 54

Products for RNF13 Gene

Sources for RNF13 Gene