Human Gene RNF111 (uc002aft.4) Description and Page Index
  Description: Homo sapiens ring finger protein 111 (RNF111), transcript variant 1, mRNA.
RefSeq Summary (NM_001270528): 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].
Transcript (Including UTRs)
   Position: hg19 chr15:59,279,865-59,389,618 Size: 109,754 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 LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:59,279,865-59,389,618)mRNA (may differ from genome)Protein (995 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIOMIMPubMedStanford SOURCE
UniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RNF111
CDC HuGE Published Literature: RNF111
Positive Disease Associations: Echocardiography , Hip
Related Studies:
  1. Echocardiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  2. Hip
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.

-  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 -171.40422-0.406 Picture PostScript Text
3' UTR -606.952519-0.241 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)
PF13445 - RING-type zinc-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

ModBase Predicted Comparative 3D Structure on H0YN55
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  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.

-  Other Names for This Gene
  Alternate Gene Symbols: H0YN55, H0YN55_HUMAN, hCG_1811968, NM_001270528, NP_001257457, uc002aft.3
UCSC ID: uc002aft.4
RefSeq Accession: NM_001270528
Protein: H0YN55 CCDS: CCDS10169.1, CCDS58365.1, CCDS58366.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001270528.1
exon count: 14CDS single in 3' UTR: no RNA size: 5929
ORF size: 2988CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6056.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.