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RNF43 ring finger protein 43 [ Homo sapiens (human) ]

Gene ID: 54894, updated on 5-Jul-2020

Summary

Official Symbol
RNF43provided by HGNC
Official Full Name
ring finger protein 43provided by HGNC
Primary source
HGNC:HGNC:18505
See related
Ensembl:ENSG00000108375 Ensembl:ENSG00000285897 MIM:612482
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
URCC; SSPCS; RNF124
Summary
The protein encoded by this gene is a RING-type E3 ubiquitin ligase and is predicted to contain a transmembrane domain, a protease-associated domain, an ectodomain, and a cytoplasmic RING domain. This protein is thought to negatively regulate Wnt signaling, and expression of this gene results in an increase in ubiquitination of frizzled receptors, an alteration in their subcellular distribution, resulting in reduced surface levels of these receptors. Mutations in this gene have been reported in multiple tumor cells, including colorectal and endometrial cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]
Expression
Broad expression in duodenum (RPKM 7.1), colon (RPKM 6.1) and 24 other tissues See more
Orthologs

Genomic context

See RNF43 in Genome Data Viewer
Location:
17q22
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (58352500..58418894, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (56431037..56494931, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene TSPOAP1, SUPT4H1 and RNF43 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory regions 8228 and 8679 Neighboring gene SPT4 homolog, DSIF elongation factor subunit Neighboring gene heat shock transcription factor 5 Neighboring gene SET pseudogene 3 Neighboring gene myotubularin related protein 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Sessile serrated polyposis cancer syndrome
MedGen: C4310714 OMIM: 617108 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide and gene-centric analyses of circulating myeloperoxidase levels in the charge and care consortia.
NHGRI GWA Catalog
Genome-wide association study of pancreatic cancer in Japanese population.
NHGRI GWA Catalog
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20315, FLJ77466, FLJ99338, MGC125630, DKFZp781H0392, DKFZp781H02126

Gene Ontology Provided by GOA

Function Evidence Code Pubs
frizzled binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
frizzled binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
Wnt receptor catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Wnt receptor catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Wnt receptor catabolic process TAS
Traceable Author Statement
more info
PubMed 
Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
stem cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
nuclear envelope IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase RNF43
Names
RING-type E3 ubiquitin transferase RNF43
NP_001292473.1
NP_001292474.1
NP_060233.3
XP_011523257.1
XP_011523258.1
XP_016880289.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042894.1 RefSeqGene

    Range
    5001..70083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1026

mRNA and Protein(s)

  1. NM_001305544.2NP_001292473.1  E3 ubiquitin-protein ligase RNF43 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001292473.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in its 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB081837, AC004687, AK000322, BC109028, CR627423
    Consensus CDS
    CCDS11607.1
    UniProtKB/Swiss-Prot
    Q68DV7
    Related
    ENSP00000462764.1, ENST00000577716.5
    Conserved Domains (4) summary
    cd16798
    Location:270316
    RING-H2_RNF43; RING finger, H2 subclass, found in RING finger protein 43 (RNF43) and similar proteins
    cl26464
    Location:570747
    Atrophin-1; Atrophin-1 family
    cl28033
    Location:312669
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
    cl28883
    Location:87186
    PA; PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. ...
  2. NM_001305545.1NP_001292474.1  E3 ubiquitin-protein ligase RNF43 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AB081837, AC004687, AK000322, AK299024, BC109028
    Consensus CDS
    CCDS82172.1
    UniProtKB/Swiss-Prot
    Q68DV7
    Related
    ENSP00000463716.1, ENST00000577625.5
    Conserved Domains (1) summary
    pfam13639
    Location:143185
    zf-RING_2; Ring finger domain
  3. NM_017763.6NP_060233.3  E3 ubiquitin-protein ligase RNF43 isoform 1 precursor

    See identical proteins and their annotated locations for NP_060233.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK000322, AK291027, BC109028, CR627423
    Consensus CDS
    CCDS11607.1
    UniProtKB/Swiss-Prot
    Q68DV7
    Related
    ENSP00000385328.2, ENST00000407977.6
    Conserved Domains (4) summary
    cd16798
    Location:270316
    RING-H2_RNF43; RING finger, H2 subclass, found in RING finger protein 43 (RNF43) and similar proteins
    cl26464
    Location:570747
    Atrophin-1; Atrophin-1 family
    cl28033
    Location:312669
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
    cl28883
    Location:87186
    PA; PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    58352500..58418894 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524956.3XP_011523258.1  E3 ubiquitin-protein ligase RNF43 isoform X2

    UniProtKB/TrEMBL
    J3KSE3
    Related
    ENSP00000462447.1, ENST00000581868.1
    Conserved Domains (1) summary
    pfam13639
    Location:143185
    zf-RING_2; Ring finger domain
  2. XM_017024800.2XP_016880289.1  E3 ubiquitin-protein ligase RNF43 isoform X1

    UniProtKB/Swiss-Prot
    Q68DV7
    Conserved Domains (2) summary
    pfam13639
    Location:270312
    zf-RING_2; Ring finger domain
    cl10459
    Location:87186
    Peptidases_S8_S53; Peptidase domain in the S8 and S53 families
  3. XM_011524955.3XP_011523257.1  E3 ubiquitin-protein ligase RNF43 isoform X1

    See identical proteins and their annotated locations for XP_011523257.1

    UniProtKB/Swiss-Prot
    Q68DV7
    Related
    ENSP00000497686.1, ENST00000648873.1
    Conserved Domains (2) summary
    pfam13639
    Location:270312
    zf-RING_2; Ring finger domain
    cl10459
    Location:87186
    Peptidases_S8_S53; Peptidase domain in the S8 and S53 families
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