Human Gene RNF220 (uc001clv.1)
  Description: Homo sapiens ring finger protein 220 (RNF220), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:44,870,960-45,117,396 Size: 246,437 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr1:44,877,770-45,116,447 Size: 238,678 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:44,870,960-45,117,396)mRNA (may differ from genome)Protein (566 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RN220_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase RNF220; EC=6.3.2.-; AltName: Full=RING finger protein 220;
FUNCTION: E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of SIN3B (By similarity).
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with SIN3B (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
PTM: Auto-ubiquitinated; leads to proteasomal degradation (By similarity).
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=BAA91704.1; 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.
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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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RNF220
CDC HuGE Published Literature: RNF220
Positive Disease Associations: Creatinine , Forced Expiratory Volume , Glomerular Filtration Rate
Related Studies:
  1. Creatinine
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
  2. Forced Expiratory Volume
    , , . [PubMed 0]
  3. Glomerular Filtration Rate
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
           more ... click here to view the complete list

-  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: 19.31 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 442.71 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 -113.69360-0.316 Picture PostScript Text
3' UTR -359.94949-0.379 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:
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF15926 - E3 ubiquitin-protein ligase RNF220

SCOP Domains:
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q5VTB9
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     
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0016567 protein ubiquitination
GO:0051865 protein autoubiquitination
GO:0090263 positive regulation of canonical Wnt signaling pathway

Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK056424 - Homo sapiens cDNA FLJ31862 fis, clone NT2RP7001335.
BC034221 - Homo sapiens ring finger protein 220, mRNA (cDNA clone MGC:39525 IMAGE:4814781), complete cds.
BC098266 - Homo sapiens ring finger protein 220, mRNA (cDNA clone MGC:120630 IMAGE:40026694), complete cds.
BC098300 - Homo sapiens ring finger protein 220, mRNA (cDNA clone MGC:120631 IMAGE:40026695), complete cds.
AK025744 - Homo sapiens cDNA: FLJ22091 fis, clone HEP16447, highly similar to AF151080 Homo sapiens HSPC246 mRNA.
AK293411 - Homo sapiens cDNA FLJ52472 complete cds.
AK297228 - Homo sapiens cDNA FLJ54701 complete cds.
JD200367 - Sequence 181391 from Patent EP1572962.
JD200351 - Sequence 181375 from Patent EP1572962.
JD272536 - Sequence 253560 from Patent EP1572962.
JD200352 - Sequence 181376 from Patent EP1572962.
JD272537 - Sequence 253561 from Patent EP1572962.
JD458522 - Sequence 439546 from Patent EP1572962.
AK296038 - Homo sapiens cDNA FLJ54815 complete cds.
AK225180 - Homo sapiens mRNA for hypothetical protein LOC55182 variant, clone: CBR05220.
AK001459 - Homo sapiens cDNA FLJ10597 fis, clone NT2RP2004802.
AK124790 - Homo sapiens cDNA FLJ42800 fis, clone BRAWH3009297.
BC073835 - Homo sapiens chromosome 1 open reading frame 164, mRNA (cDNA clone IMAGE:5170310).
AK124639 - Homo sapiens cDNA FLJ42648 fis, clone BRACE3027242.
JD094687 - Sequence 75711 from Patent EP1572962.
JD352226 - Sequence 333250 from Patent EP1572962.
JD296283 - Sequence 277307 from Patent EP1572962.
BC062600 - Homo sapiens cDNA clone IMAGE:5406896, partial cds.
JD370456 - Sequence 351480 from Patent EP1572962.
JD335631 - Sequence 316655 from Patent EP1572962.
JD495457 - Sequence 476481 from Patent EP1572962.
JD280276 - Sequence 261300 from Patent EP1572962.
JD318625 - Sequence 299649 from Patent EP1572962.
JD253189 - Sequence 234213 from Patent EP1572962.
JD280275 - Sequence 261299 from Patent EP1572962.
JD224282 - Sequence 205306 from Patent EP1572962.
JD174329 - Sequence 155353 from Patent EP1572962.
JD480748 - Sequence 461772 from Patent EP1572962.
JD210039 - Sequence 191063 from Patent EP1572962.
AF151080 - Homo sapiens HSPC246 mRNA, complete cds.
JD500243 - Sequence 481267 from Patent EP1572962.
JD223192 - Sequence 204216 from Patent EP1572962.
JD484476 - Sequence 465500 from Patent EP1572962.
JD475164 - Sequence 456188 from Patent EP1572962.
JD343327 - Sequence 324351 from Patent EP1572962.
BC105790 - Homo sapiens cDNA clone IMAGE:6457164.
JD407747 - Sequence 388771 from Patent EP1572962.
BC000279 - Homo sapiens ring finger protein 220, mRNA (cDNA clone IMAGE:3357957), complete cds.
JD090996 - Sequence 72020 from Patent EP1572962.
KJ904794 - Synthetic construct Homo sapiens clone ccsbBroadEn_14188 RNF220 gene, encodes complete protein.
JD068414 - Sequence 49438 from Patent EP1572962.
JD216020 - Sequence 197044 from Patent EP1572962.
JD484358 - Sequence 465382 from Patent EP1572962.
JD214987 - Sequence 196011 from Patent EP1572962.
JD052633 - Sequence 33657 from Patent EP1572962.
JD197217 - Sequence 178241 from Patent EP1572962.
JD283473 - Sequence 264497 from Patent EP1572962.

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

Protein Q5VTB9 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B3KPJ3, C1orf164, NM_018150, NP_060620, Q4KMX2, Q5VTB9, Q9NVP6, RN220_HUMAN
UCSC ID: uc001clv.1
RefSeq Accession: NM_018150
Protein: Q5VTB9 (aka RN220_HUMAN)
CCDS: CCDS510.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018150.2
exon count: 15CDS single in 3' UTR: no RNA size: 3025
ORF size: 1701CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3308.50frame shift in genome: no % Coverage: 99.50
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.