Human Gene RNF111 (ENST00000348370.9_11) from GENCODE V47lift37
  Description: ring finger protein 111, transcript variant 2 (from RefSeq NM_017610.8)
Gencode Transcript: ENST00000348370.9_11
Gencode Gene: ENSG00000157450.16_17
Transcript (Including UTRs)
   Position: hg19 chr15:59,279,862-59,389,618 Size: 109,757 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr15:59,323,022-59,387,099 Size: 64,078 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:59,279,862-59,389,618)mRNA (may differ from genome)Protein (986 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RN111_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase Arkadia; EC=6.3.2.-; AltName: Full=RING finger protein 111;
FUNCTION: Acts in the NODAL pathway of mesoderm patterning during embryonic development. Acts downstream AXIN1 as an E3 ubiquitin- protein ligase which promotes the ubiquitination of inhibitory SMADs such as SMAD7, induces their proteasomal degradation and thereby enhances the transcriptional activity of TGF-beta and BMP. Activates Smad3/Smad4-dependent transcription by triggering signal-induced SnoN degradation.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with SMAD6, SMAD7, AXIN1, AXIN2 and SKIL isoform SNON. Part of a complex containing RNF111, AXIN1 and SMAD7.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Upon TGF-beta treatment, translocates from nucleus to cytosol.
TISSUE SPECIFICITY: Broadly expressed.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=AAH10369.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC04531.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAD18633.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.78 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 238.40 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -171.10425-0.403 Picture PostScript Text
3' UTR -571.102519-0.227 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF13639 - Ring finger domain
PF13920 - Zinc finger, C3HC4 type (RING finger)
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF15303 - E3 ubiquitin-protein ligase Arkadia N-terminus
PF17123 - RING-like zinc finger

SCOP Domains:
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2KIZ - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q6ZNA4
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0032184 SUMO polymer binding
GO:0046332 SMAD binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0007275 multicellular organism development
GO:0007389 pattern specification process
GO:0016567 protein ubiquitination
GO:0030511 positive regulation of transforming growth factor beta receptor signaling pathway
GO:0030579 ubiquitin-dependent SMAD protein catabolic process
GO:0031398 positive regulation of protein ubiquitination
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0070911 global genome nucleotide-excision repair

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016605 PML body
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  BC060862 - Homo sapiens ring finger protein 111, mRNA (cDNA clone MGC:71797 IMAGE:30336202), complete cds.
BX538130 - Homo sapiens mRNA; cDNA DKFZp686H1966 (from clone DKFZp686H1966); complete cds.
LF384562 - JP 2014500723-A/192065: Polycomb-Associated Non-Coding RNAs.
BX647259 - Homo sapiens mRNA; cDNA DKFZp686L1262 (from clone DKFZp686L1262).
AK131304 - Homo sapiens cDNA FLJ16278 fis, clone NT2RI3001132, highly similar to Mus musculus Arkadia (Arkadia) mRNA.
KJ902684 - Synthetic construct Homo sapiens clone ccsbBroadEn_12078 RNF111 gene, encodes complete protein.
AK131488 - Homo sapiens cDNA FLJ16671 fis, clone THYMU3001428.
AL832089 - Homo sapiens mRNA; cDNA DKFZp313E0731 (from clone DKFZp313E0731).
AK095327 - Homo sapiens cDNA FLJ38008 fis, clone CTONG2012452, highly similar to Mus musculus Arkadia (Arkadia) mRNA.
BC020984 - Homo sapiens ring finger protein 111, mRNA (cDNA clone IMAGE:3851753), partial cds.
MA620139 - JP 2018138019-A/192065: Polycomb-Associated Non-Coding RNAs.
CU687480 - Synthetic construct Homo sapiens gateway clone IMAGE:100021051 5' read RNF111 mRNA.
LF377550 - JP 2014500723-A/185053: Polycomb-Associated Non-Coding RNAs.
JD027416 - Sequence 8440 from Patent EP1572962.
JD036001 - Sequence 17025 from Patent EP1572962.
LF377545 - JP 2014500723-A/185048: Polycomb-Associated Non-Coding RNAs.
JD026941 - Sequence 7965 from Patent EP1572962.
JD552462 - Sequence 533486 from Patent EP1572962.
JD345882 - Sequence 326906 from Patent EP1572962.
JD512159 - Sequence 493183 from Patent EP1572962.
MA613127 - JP 2018138019-A/185053: Polycomb-Associated Non-Coding RNAs.
MA613122 - JP 2018138019-A/185048: Polycomb-Associated Non-Coding RNAs.
BC010369 - Homo sapiens ring finger protein 111, mRNA (cDNA clone IMAGE:4049734), complete cds.
AL157474 - Homo sapiens mRNA; cDNA DKFZp761D081 (from clone DKFZp761D081).
KJ902683 - Synthetic construct Homo sapiens clone ccsbBroadEn_12077 RNF111 gene, encodes complete protein.
DQ583506 - Homo sapiens piRNA piR-50618, complete sequence.
LF377537 - JP 2014500723-A/185040: Polycomb-Associated Non-Coding RNAs.
JD192395 - Sequence 173419 from Patent EP1572962.
JD398053 - Sequence 379077 from Patent EP1572962.
JD113420 - Sequence 94444 from Patent EP1572962.
JD402519 - Sequence 383543 from Patent EP1572962.
JD113708 - Sequence 94732 from Patent EP1572962.
JD181042 - Sequence 162066 from Patent EP1572962.
JD563299 - Sequence 544323 from Patent EP1572962.
JD489575 - Sequence 470599 from Patent EP1572962.
LF377536 - JP 2014500723-A/185039: Polycomb-Associated Non-Coding RNAs.
JD284229 - Sequence 265253 from Patent EP1572962.
JD353837 - Sequence 334861 from Patent EP1572962.
LF377535 - JP 2014500723-A/185038: Polycomb-Associated Non-Coding RNAs.
LF377534 - JP 2014500723-A/185037: Polycomb-Associated Non-Coding RNAs.
JD052951 - Sequence 33975 from Patent EP1572962.
LF377533 - JP 2014500723-A/185036: Polycomb-Associated Non-Coding RNAs.
JD327793 - Sequence 308817 from Patent EP1572962.
JD473382 - Sequence 454406 from Patent EP1572962.
LF377532 - JP 2014500723-A/185035: Polycomb-Associated Non-Coding RNAs.
JD415458 - Sequence 396482 from Patent EP1572962.
LQ283612 - Sequence 69 from Patent WO2016034611.
JD090509 - Sequence 71533 from Patent EP1572962.
JD189556 - Sequence 170580 from Patent EP1572962.
MA613114 - JP 2018138019-A/185040: Polycomb-Associated Non-Coding RNAs.
MA613113 - JP 2018138019-A/185039: Polycomb-Associated Non-Coding RNAs.
MA613112 - JP 2018138019-A/185038: Polycomb-Associated Non-Coding RNAs.
MA613111 - JP 2018138019-A/185037: Polycomb-Associated Non-Coding RNAs.
MA613110 - JP 2018138019-A/185036: Polycomb-Associated Non-Coding RNAs.
MA613109 - JP 2018138019-A/185035: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6ZNA4 (Reactome details) participates in the following event(s):

R-HSA-2186771 RNF111 binds SMAD7
R-HSA-2186785 RNF111 ubiquitinates SMAD7
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-2186741 SMAD2/3 activation induces binding of RNF111/SMURF2 to SKI/SKIL
R-HSA-2186747 Ubiquitination of SKI/SKIL by RNF111/SMURF2
R-HSA-6790487 RNF111 ubiquitinates SUMOylated XPC
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-2173793 Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
R-HSA-5696395 Formation of Incision Complex in GG-NER
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-212436 Generic Transcription Pathway
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-1280218 Adaptive Immune System
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-168256 Immune System
R-HSA-162582 Signal Transduction
R-HSA-74160 Gene expression (Transcription)
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: C9JUS4, ENST00000348370.1, ENST00000348370.2, ENST00000348370.3, ENST00000348370.4, ENST00000348370.5, ENST00000348370.6, ENST00000348370.7, ENST00000348370.8, H0YN55, NM_017610, Q6P9A4, Q6ZMU2, Q6ZNA4, Q7L428, Q7Z346, Q8N1P9, Q8WUA3, Q9NSR1, RN111_HUMAN, RNF111 , uc317xqz.1, uc317xqz.2
UCSC ID: ENST00000348370.9_11
RefSeq Accession: NM_017610.8
Protein: Q6ZNA4 (aka RN111_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.