Human Gene RNF180 (uc003jti.3) Description and Page Index
  Description: Homo sapiens ring finger protein 180 (RNF180), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:63,461,671-63,668,696 Size: 207,026 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr5:63,496,635-63,665,641 Size: 169,007 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:63,461,671-63,668,696)mRNA (may differ from genome)Protein (592 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RN180_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase RNF180; EC=6.3.2.-; AltName: Full=RING finger protein 180;
FUNCTION: E3 ubiquitin-protein ligase which promotes polyubiquitination and degradation by the proteasome pathway of ZIC2 (By similarity).
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with ZIC2 (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass membrane protein. Nucleus envelope (By similarity).
DOMAIN: The RING-type zinc finger domain mediates polyubiquitination of the interacting protein.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=CAD89939.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RNF180
CDC HuGE Published Literature: RNF180

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.00 RPKM in Artery - Tibial
Total median expression: 99.47 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.40110-0.495 Picture PostScript Text
3' UTR -619.053055-0.203 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
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF13445 - RING-type zinc-finger
PF13920 - Zinc finger, C3HC4 type (RING finger)

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

ModBase Predicted Comparative 3D Structure on Q86T96
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016740 transferase activity
GO:0031624 ubiquitin conjugating enzyme binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0016567 protein ubiquitination
GO:0030534 adult behavior
GO:0031398 positive regulation of protein ubiquitination
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0042415 norepinephrine metabolic process
GO:0042428 serotonin metabolic process
GO:0050790 regulation of catalytic activity
GO:1901360 organic cyclic compound metabolic process

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031227 intrinsic component of endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  AL832580 - Homo sapiens mRNA; cDNA DKFZp451F1716 (from clone DKFZp451F1716).
AB527207 - Synthetic construct DNA, clone: pF1KE0019, Homo sapiens RNF180 gene for ring finger protein 180, without stop codon, in Flexi system.
AM393544 - Synthetic construct Homo sapiens clone IMAGE:100002245 for hypothetical protein (RNF180 gene).
AK090756 - Homo sapiens cDNA FLJ33437 fis, clone BRACE2021541, weakly similar to PROTEIN-TYROSINE PHOSPHATASE YVH1 (EC 3.1.3.48).
AX746601 - Sequence 126 from Patent EP1308459.
BC101278 - Homo sapiens ring finger protein 180, mRNA (cDNA clone MGC:120326 IMAGE:40024390), complete cds.
BC101279 - Homo sapiens ring finger protein 180, mRNA (cDNA clone IMAGE:40024391), complete cds.
BC101277 - Homo sapiens ring finger protein 180, mRNA (cDNA clone MGC:120325 IMAGE:40024386), complete cds.
BC101397 - Homo sapiens ring finger protein 180, mRNA (cDNA clone MGC:120328 IMAGE:40024392), complete cds.
KJ896011 - Synthetic construct Homo sapiens clone ccsbBroadEn_05405 RNF180 gene, encodes complete protein.
JD553401 - Sequence 534425 from Patent EP1572962.
JD235101 - Sequence 216125 from Patent EP1572962.
JD346165 - Sequence 327189 from Patent EP1572962.
JD101734 - Sequence 82758 from Patent EP1572962.
JD183525 - Sequence 164549 from Patent EP1572962.
JD312927 - Sequence 293951 from Patent EP1572962.
JD095737 - Sequence 76761 from Patent EP1572962.
JD245940 - Sequence 226964 from Patent EP1572962.
JD084636 - Sequence 65660 from Patent EP1572962.
JD433764 - Sequence 414788 from Patent EP1572962.
JD562709 - Sequence 543733 from Patent EP1572962.
JD509545 - Sequence 490569 from Patent EP1572962.
JD270980 - Sequence 252004 from Patent EP1572962.
JD359294 - Sequence 340318 from Patent EP1572962.
JD359233 - Sequence 340257 from Patent EP1572962.
JD306087 - Sequence 287111 from Patent EP1572962.
JD315610 - Sequence 296634 from Patent EP1572962.
JD231202 - Sequence 212226 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001113561, NP_001107033, Q0JSU3, Q495A8, Q86T96, Q8NBD1, RN180_HUMAN
UCSC ID: uc003jti.3
RefSeq Accession: NM_001113561
Protein: Q86T96 (aka RN180_HUMAN)
CCDS: CCDS47219.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001113561.1
exon count: 8CDS single in 3' UTR: no RNA size: 4944
ORF size: 1779CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3658.00frame 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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.