Format

Send to:

Choose Destination

RNF111 ring finger protein 111 [ Homo sapiens (human) ]

Gene ID: 54778, updated on 7-Jul-2019

Summary

Official Symbol
RNF111provided by HGNC
Official Full Name
ring finger protein 111provided by HGNC
Primary source
HGNC:HGNC:17384
See related
Ensembl:ENSG00000157450 MIM:605840
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
ARK; hRNF111
Summary
The protein encoded by this gene is a nuclear RING-domain containing E3 ubiquitin ligase. This protein interacts with the transforming growth factor (TGF) -beta/NODAL signaling pathway by promoting the ubiquitination and proteosomal degradation of negative regulators, like SMAD proteins, and thereby enhances TGF-beta target-gene transcription. As a modulator of the nodal signaling cascade, this gene plays a critical role in the induction of mesoderm during embryonic development. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]
Expression
Ubiquitous expression in thyroid (RPKM 5.8), brain (RPKM 5.5) and 25 other tissues See more
Orthologs

Genomic context

See RNF111 in Genome Data Viewer
Location:
15q22.1-q22.2
Exon count:
17
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (58987588..59097419)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (59279865..59389618)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene SAFB like transcription modulator Neighboring gene ribosome binding factor A (putative) pseudogene Neighboring gene ribosomal protein L21 pseudogene 113 Neighboring gene Sharpr-MPRA regulatory region 4265 Neighboring gene cyclin B2 Neighboring gene myosin IE

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Common variation contributes to the genetic architecture of social communication traits.
NHGRI GWA Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
NHGRI GWA Catalog
Variants in several genomic regions associated with asperger disorder.
NHGRI GWA Catalog

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystem (from REACTOME)
    Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystemIntracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T ...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Downregulation of SMAD2/3:SMAD4 transcriptional activity, organism-specific biosystem (from REACTOME)
    Downregulation of SMAD2/3:SMAD4 transcriptional activity, organism-specific biosystemTranscriptional activity of SMAD2/3:SMAD4 heterotrimer can be inhibited by formation of a complex with SKI or SKIL (SNO), where SKI or SKIL recruit NCOR and possibly other transcriptional repressors ...
  • Formation of Incision Complex in GG-NER, organism-specific biosystem (from REACTOME)
    Formation of Incision Complex in GG-NER, organism-specific biosystemAfter the XPC complex and the UV-DDB complex bind damaged DNA, a basal transcription factor TFIIH is recruited to the nucleotide excision repair (NER) site (Volker et al. 2001, Riedl et al. 2003). DN...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
    Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription, organism-specific biosystem (from REACTOME)
    SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription, organism-specific biosystemAfter phosphorylated SMAD2 and/or SMAD3 form a heterotrimer with SMAD4, SMAD2/3:SMAD4 complex translocates to the nucleus (Xu et al. 2000, Kurisaki et al. 2001, Xiao et al. 2003). In the nucleus, lin...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by TGF-beta Receptor Complex, organism-specific biosystem (from REACTOME)
    Signaling by TGF-beta Receptor Complex, organism-specific biosystemThe TGF-beta/BMP pathway incorporates several signaling pathways that share most, but not all, components of a central signal transduction engine. The general signaling scheme is rather simple: upon ...
  • TGF-beta Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TGF-beta Signaling Pathway, organism-specific biosystemThe signal transduction mechanisms underlying the pathophysiological activities of transforming growth factor-? (TGF-?) have been extensively studied since its discovery nearly 30 years ago. TGF-? li...
  • TGF-beta receptor signaling, organism-specific biosystem (from Pathway Interaction Database)
    TGF-beta receptor signaling, organism-specific biosystem
    TGF-beta receptor signaling
  • Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer, organism-specific biosystem (from REACTOME)
    Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer, organism-specific biosystemIn the nucleus, SMAD2/3:SMAD4 heterotrimer complex acts as a transcriptional regulator. The activity of SMAD2/3 complex is regulated both positively and negatively by association with other transcrip...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ38008, DKFZp761D081, DKFZp313E0731, DKFZp686H1966

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SMAD binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SUMO polymer binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SUMO polymer binding IDA
Inferred from Direct Assay
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
global genome nucleotide-excision repair TAS
Traceable Author Statement
more info
 
pattern specification process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
positive regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transforming growth factor beta receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein polyubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent SMAD protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
PML body IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 
protein-containing complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase Arkadia
Names
Arkadia
RING-type E3 ubiquitin transferase Arkadia
NP_001257457.1
NP_001257458.1
NP_001257459.1
NP_001317260.1
NP_060080.6
XP_006720638.1
XP_006720642.1
XP_011519996.2
XP_011519998.2
XP_011519999.2
XP_011520001.2
XP_016877825.1
XP_016877826.1
XP_016877827.1
XP_016877828.1
XP_016877829.1
XP_016877830.1
XP_016877831.1
XP_016877832.1

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.

mRNA and Protein(s)

  1. NM_001270528.2NP_001257457.1  E3 ubiquitin-protein ligase Arkadia isoform 1

    See identical proteins and their annotated locations for NP_001257457.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC025918, AI189975, AL157474, AL832089, BM986870, BX538130, BX647259, CN420669, N24855
    Consensus CDS
    CCDS58365.1
    UniProtKB/Swiss-Prot
    Q6ZNA4
    Related
    ENSP00000453872.1, ENST00000559209.5
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:943984
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  2. NM_001270529.2NP_001257458.1  E3 ubiquitin-protein ligase Arkadia isoform 3

    See identical proteins and their annotated locations for NP_001257458.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AC025918, AI189975, AL157474, BC060862, BM986870, BX538130, BX647259, CN420669, N24855
    UniProtKB/Swiss-Prot
    Q6ZNA4
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:933974
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  3. NM_001270530.1NP_001257459.1  E3 ubiquitin-protein ligase Arkadia isoform 4

    See identical proteins and their annotated locations for NP_001257459.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AI189975, AL832089, BC020984, BM986870, BX538130, BX647259, CN420669, DA720863, N24855
    Consensus CDS
    CCDS58366.1
    UniProtKB/Swiss-Prot
    Q6ZNA4
    Related
    ENSP00000452732.1, ENST00000557998.5
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:942983
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  4. NM_001330331.2NP_001317260.1  E3 ubiquitin-protein ligase Arkadia isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (5) is longer than isoform 1.
    Source sequence(s)
    AC025918, AC092757, AI189975
    Consensus CDS
    CCDS81888.1
    UniProtKB/Swiss-Prot
    Q6ZNA4
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:951992
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  5. NM_017610.8NP_060080.6  E3 ubiquitin-protein ligase Arkadia isoform 2

    See identical proteins and their annotated locations for NP_060080.6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC025918, AI189975, AL157474, AL832089, BM986870, BX538130, BX647259, CN420669, N24855
    Consensus CDS
    CCDS10169.1
    UniProtKB/Swiss-Prot
    Q6ZNA4
    UniProtKB/TrEMBL
    A0A024R5T5
    Related
    ENSP00000288199.5, ENST00000348370.8
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:934975
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus

RefSeqs of Annotated Genomes: Homo sapiens 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_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    58987588..59097419
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022338.2XP_016877827.1  E3 ubiquitin-protein ligase Arkadia isoform X9

    UniProtKB/Swiss-Prot
    Q6ZNA4
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:942983
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  2. XM_006720575.3XP_006720638.1  E3 ubiquitin-protein ligase Arkadia isoform X5

    Conserved Domains (3) summary
    pfam05647
    Location:430494
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:9741015
    zf-RING_2; Ring finger domain
    pfam15303
    Location:41274
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  3. XM_017022337.2XP_016877826.1  E3 ubiquitin-protein ligase Arkadia isoform X8

    Conserved Domains (3) summary
    pfam05647
    Location:407471
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:950991
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  4. XM_017022339.2XP_016877828.1  E3 ubiquitin-protein ligase Arkadia isoform X10

  5. XM_017022340.2XP_016877829.1  E3 ubiquitin-protein ligase Arkadia isoform X11

    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:941982
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  6. XM_017022336.1XP_016877825.1  E3 ubiquitin-protein ligase Arkadia isoform X6

  7. XM_017022341.1XP_016877830.1  E3 ubiquitin-protein ligase Arkadia isoform X11

    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:941982
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  8. XM_017022343.1XP_016877832.1  E3 ubiquitin-protein ligase Arkadia isoform X13

    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:933974
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  9. XM_006720579.3XP_006720642.1  E3 ubiquitin-protein ligase Arkadia isoform X7

    See identical proteins and their annotated locations for XP_006720642.1

    UniProtKB/Swiss-Prot
    Q6ZNA4
    Related
    ENSP00000453015.1, ENST00000561186.5
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:951992
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  10. XM_017022342.1XP_016877831.1  E3 ubiquitin-protein ligase Arkadia isoform X12

    UniProtKB/TrEMBL
    A0A024R5T5
    Conserved Domains (3) summary
    pfam05647
    Location:407474
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
    pfam13639
    Location:934975
    zf-RING_2; Ring finger domain
    pfam15303
    Location:18251
    RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
  11. XM_011521694.2XP_011519996.2  E3 ubiquitin-protein ligase Arkadia isoform X4

  12. XM_011521696.2XP_011519998.2  E3 ubiquitin-protein ligase Arkadia isoform X1

  13. XM_011521697.3XP_011519999.2  E3 ubiquitin-protein ligase Arkadia isoform X2

  14. XM_011521699.2XP_011520001.2  E3 ubiquitin-protein ligase Arkadia isoform X3

Support Center