The protein encoded by this gene contains a C-terminal RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions, and an N-terminal SPRY domain. This protein displays E3 ubiquitin ligase activity toward the cyclin-dependent kinase inhibitor 1B which is also known as p27 or KIP1. Al... See more...

Aliases for RNF123 Gene

Aliases for RNF123 Gene

  • Ring Finger Protein 123 2 3 5
  • KPC1 2 3 4
  • Kip1 Ubiquitination-Promoting Complex Subunit 1 2 3
  • Kip1 Ubiquitination-Promoting Complex Protein 1 3 4
  • RING-Type E3 Ubiquitin Transferase RNF123 3 4
  • E3 Ubiquitin-Protein Ligase RNF123 3 4
  • RING Finger Protein 123 4
  • EC 2.3.2.27 4
  • FLJ12565 2
  • FP1477 3
  • RNF123 5

External Ids for RNF123 Gene

Previous GeneCards Identifiers for RNF123 Gene

  • GC03P049581
  • GC03P049685
  • GC03P049701
  • GC03P049726

Summaries for RNF123 Gene

Entrez Gene Summary for RNF123 Gene

  • The protein encoded by this gene contains a C-terminal RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions, and an N-terminal SPRY domain. This protein displays E3 ubiquitin ligase activity toward the cyclin-dependent kinase inhibitor 1B which is also known as p27 or KIP1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

GeneCards Summary for RNF123 Gene

RNF123 (Ring Finger Protein 123) is a Protein Coding gene. Among its related pathways are Class I MHC mediated antigen processing and presentation and Deubiquitination. Gene Ontology (GO) annotations related to this gene include ligase activity. An important paralog of this gene is RSPRY1.

UniProtKB/Swiss-Prot Summary for RNF123 Gene

  • Catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase. Promotes the ubiquitination and proteasome-mediated degradation of CDKN1B which is the cyclin-dependent kinase inhibitor at the G0-G1 transition of the cell cycle (PubMed:15531880, PubMed:16227581). Functions also as an inhibitor of innate antiviral signaling mediated by DDX58 and IFIH1 independently of its E3 ligase activity (PubMed:27312109). Interacts with the N-terminal CARD domains of DDX58 and IFIH1 and competes with the downstream adapter MAVS (PubMed:27312109).

Gene Wiki entry for RNF123 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RNF123 Gene

Genomics for RNF123 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RNF123 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
GH03J049685 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 -0.3 -275 5.4 BCLAF1 SP1 ZNF207 NCOR1 ZNF600 ZNF580 ZNF592 CEBPA ZSCAN16 ZIC2 MST1 HSALNG0025959 RNF123 lnc-MST1-1 piR-46140 AMT RBM6 QRICH1 CDHR4 AMIGO3
GH03J049747 Enhancer 0.9 Ensembl ENCODE 12.1 +59.6 59645 1.9 CEBPA THAP11 SAP130 TEAD3 FOSL2 JUND SOX5 HNF4A HMG20A ATF4 INKA1 ENSG00000244730 IP6K1 GMPPB AMIGO3 RNF123 BSN-AS1 BSN BSN-DT RF00998-091
GH03J050297 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 4.3 +612.2 612162 6.5 BCLAF1 ZNF207 MYC IKZF1 ZNF600 SSRP1 ZNF592 ATF2 KLF9 CEBPA HYAL3 HYAL1 NAA80 lnc-HYAL3-1 RBM6 AMT RHOA-IT1 TMEM115 SEMA3F-AS1 HEMK1
GH03J049771 Enhancer 0.4 Ensembl 11.8 +83.0 83049 0.8 PRDM6 RUNX3 PRDM1 CDHR4 INKA1 UBA7 GMPPB AMIGO3 RNF123 TRAIP MON1A RBM6 PHF5EP
GH03J049750 Enhancer 0.2 Ensembl 12.1 +62.8 62848 0.8 INKA1 ENSG00000244730 IP6K1 GMPPB AMIGO3 RNF123 BSN BSN-AS1 COX6CP14 RF00998-091
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNF123 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RNF123

Top Transcription factor binding sites by QIAGEN in the RNF123 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • HFH-3
  • LCR-F1
  • Nkx2-5
  • SEF-1 (1)

Genomic Locations for RNF123 Gene

Latest Assembly
chr3:49,688,753-49,721,529
(GRCh38/hg38)
Size:
32,777 bases
Orientation:
Plus strand

Previous Assembly
chr3:49,726,990-49,758,962
(GRCh37/hg19 by Entrez Gene)
Size:
31,973 bases
Orientation:
Plus strand

chr3:49,726,932-49,758,962
(GRCh37/hg19 by Ensembl)
Size:
32,031 bases
Orientation:
Plus strand

Genomic View for RNF123 Gene

Genes around RNF123 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF123 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF123 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF123 Gene

Proteins for RNF123 Gene

  • Protein details for RNF123 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5XPI4-RN123_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF123
    Protein Accession:
    Q5XPI4
    Secondary Accessions:
    • A1L4Q3
    • A6NLS5
    • Q5I022
    • Q6PFW4
    • Q71RH0
    • Q8IW18
    • Q9H0M8
    • Q9H5L8
    • Q9H9T2

    Protein attributes for RNF123 Gene

    Size:
    1314 amino acids
    Molecular mass:
    148515 Da
    Quaternary structure:
    • Component of the KPC complex composed of RNF123/KPC1 and UBAC1/KPC2. Interacts with UBAC1 and CDKN1B via its N-terminal domain. Interacts with DDX58 (via N-terminus) and IFIH1 (via N-terminus).
    SequenceCaution:
    • Sequence=BAB14139.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB15607.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RNF123 Gene

    Alternative splice isoforms for RNF123 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF123 Gene

Post-translational modifications for RNF123 Gene

  • Ubiquitinated, leading to its degradation. Deubiquitinated by USP19, thereby stimulating CDKN1B ubiquitin-dependent degradation.
  • Ubiquitination at Lys33, Lys467, Lys530, Lys704, Lys806, Lys814, Lys906, and Lys1286
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RNF123 Gene

Domains & Families for RNF123 Gene

Gene Families for RNF123 Gene

Protein Domains for RNF123 Gene

Suggested Antigen Peptide Sequences for RNF123 Gene

GenScript: Design optimal peptide antigens:
  • RING finger protein 123 (RN123_HUMAN)
genes like me logo Genes that share domains with RNF123: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RNF123 Gene

Function for RNF123 Gene

Molecular function for RNF123 Gene

UniProtKB/Swiss-Prot Function:
Catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase. Promotes the ubiquitination and proteasome-mediated degradation of CDKN1B which is the cyclin-dependent kinase inhibitor at the G0-G1 transition of the cell cycle (PubMed:15531880, PubMed:16227581). Functions also as an inhibitor of innate antiviral signaling mediated by DDX58 and IFIH1 independently of its E3 ligase activity (PubMed:27312109). Interacts with the N-terminal CARD domains of DDX58 and IFIH1 and competes with the downstream adapter MAVS (PubMed:27312109).
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 RNF123 Gene

Phenotypes From GWAS Catalog for RNF123 Gene

Gene Ontology (GO) - Molecular Function for RNF123 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IBA 21873635
GO:0005515 protein binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RNF123: view
genes like me logo Genes that share phenotypes with RNF123: view

miRNA for RNF123 Gene

miRTarBase miRNAs that target RNF123

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RNF123

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RNF123 Gene

Localization for RNF123 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF123 Gene

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 RNF123 gene
Compartment Confidence
nucleus 4
cytosol 4
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RNF123 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0005829 cytosol TAS --
GO:0031965 nuclear membrane IDA --
genes like me logo Genes that share ontologies with RNF123: view

Pathways & Interactions for RNF123 Gene

genes like me logo Genes that share pathways with RNF123: view

UniProtKB/Swiss-Prot Q5XPI4-RN123_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RNF123 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
GO:0016579 protein deubiquitination TAS --
GO:0051603 proteolysis involved in cellular protein catabolic process IBA 21873635
genes like me logo Genes that share ontologies with RNF123: view

No data available for SIGNOR curated interactions for RNF123 Gene

Drugs & Compounds for RNF123 Gene

No Compound Related Data Available

Transcripts for RNF123 Gene

mRNA/cDNA for RNF123 Gene

1 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
14 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 RNF123

Alternative Splicing Database (ASD) splice patterns (SP) for RNF123 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b · 20c ^
SP1:
SP2:
SP3:
SP4: -
SP5:
SP6: -
SP7: -
SP8:
SP9:
SP10:

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:

Relevant External Links for RNF123 Gene

GeneLoc Exon Structure for
RNF123

Expression for RNF123 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RNF123 Gene

mRNA differential expression in normal tissues according to GTEx for RNF123 Gene

This gene is overexpressed in Muscle - Skeletal (x7.4).

Protein differential expression in normal tissues from HIPED for RNF123 Gene

This gene is overexpressed in Lymph node (10.1), Heart (7.2), and Tonsil (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RNF123 Gene



Protein tissue co-expression partners for RNF123 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RNF123

SOURCE GeneReport for Unigene cluster for RNF123 Gene:

Hs.553723

Evidence on tissue expression from TISSUES for RNF123 Gene

  • Nervous system(4.9)
  • Lung(4.2)
  • Eye(4.1)
  • Muscle(3)
genes like me logo Genes that share expression patterns with RNF123: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF123 Gene

Orthologs for RNF123 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RNF123 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RNF123 29
  • 98.16 (n)
Dog
(Canis familiaris)
Mammalia RNF123 29 30
  • 90.84 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RNF123 29 30
  • 89.26 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rnf123 29 16 30
  • 89.09 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rnf123 29
  • 88.59 (n)
Oppossum
(Monodelphis domestica)
Mammalia RNF123 30
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RNF123 30
  • 72 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RNF123 29 30
  • 76.09 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RNF123 30
  • 80 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rnf123 29
  • 71.3 (n)
Str.7038 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.10089 29
Zebrafish
(Danio rerio)
Actinopterygii rnf123 30
  • 78 (a)
OneToOne
LOC101884269 29
  • 72.88 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG6752 29 30
  • 47.34 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009295 29
  • 26.27 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons RKP 29
  • 41.17 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 11 (a)
OneToOne
Species where no ortholog for RNF123 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for RNF123 Gene

ENSEMBL:
Gene Tree for RNF123 (if available)
TreeFam:
Gene Tree for RNF123 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RNF123: view image
Alliance of Genome Resources:
Additional Orthologs for RNF123

Paralogs for RNF123 Gene

Paralogs for RNF123 Gene

genes like me logo Genes that share paralogs with RNF123: view

Variants for RNF123 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RNF123 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
1013476 Likely Benign: not provided 49,720,876(+) G/A
NM_021971.4(GMPPB):c.*876C>T
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,THREE_PRIME_UTR
801351 Uncertain Significance: Hypertrophic cardiomyopathy 49,716,468(+) C/T
NM_022064.5(RNF123):c.3491C>T (p.Pro1164Leu)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs61745258 Benign: not provided 49,702,671(+) C/T
NM_022064.5(RNF123):c.1668C>T (p.Cys556=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs74959466 Benign: not provided 49,720,606(+) G/C
NM_022064.5(RNF123):c.3596G>C (p.Gly1199Ala)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,THREE_PRIME_UTR
rs2960546 -- p.Pro51Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RNF123 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 RNF123 Gene

Variant ID Type Subtype PubMed ID
esv28815 CNV gain+loss 19812545
nsv1118699 CNV duplication 24896259
nsv1141429 CNV duplication 24896259
nsv1148681 CNV duplication 26484159
nsv482082 CNV gain 20164927
nsv508217 CNV deletion 20534489
nsv820990 CNV duplication 20802225
nsv822077 CNV gain 20364138
nsv979829 CNV duplication 23825009

Variation tolerance for RNF123 Gene

Residual Variation Intolerance Score: 22.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.65; 72.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF123 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF123
Leiden Open Variation Database (LOVD)
RNF123

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF123 Gene

Disorders for RNF123 Gene

Additional Disease Information for RNF123

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for RNF123 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNF123 Gene

Publications for RNF123 Gene

  1. Role of the UBL-UBA protein KPC2 in degradation of p27 at G1 phase of the cell cycle. (PMID: 16227581) Hara T … Nakayama KI (Molecular and cellular biology 2005) 3 4 22
  2. Cytoplasmic ubiquitin ligase KPC regulates proteolysis of p27(Kip1) at G1 phase. (PMID: 15531880) Kamura T … Nakayama KI (Nature cell biology 2004) 2 3 4
  3. RNF123 has an E3 ligase-independent function in RIG-I-like receptor-mediated antiviral signaling. (PMID: 27312109) Wang S … Chen DY (EMBO reports 2016) 3 4
  4. Association analysis of 3p21 with Crohn's disease in a New Zealand population. (PMID: 20307617) Morgan AR … Ferguson LR (Human immunology 2010) 3 40
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for RNF123 Gene

Sources for RNF123 Gene