Human Gene RNF187 (uc001htb.3)
  Description: Homo sapiens ring finger protein 187 (RNF187), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:228,675,068-228,683,889 Size: 8,822 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr1:228,675,193-228,681,586 Size: 6,394 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:228,675,068-228,683,889)mRNA (may differ from genome)Protein (235 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RN187_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase RNF187; EC=6.3.2.-; AltName: Full=RING domain AP1 coactivator 1; Short=RACO-1; AltName: Full=RING finger protein 187;
FUNCTION: E3 ubiquitin-protein ligase that acts as a coactivator of JUN-mediated gene activation in response to growth factor signaling via the MAP3K1 pathway, independently from MAPK8.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with JUN, independently of JUN phosphorylation.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Predominantly located in the cytoplasm. Shuttles between the cytoplasm and the nucleus.
DOMAIN: The RING-type zinc finger domain is required for E3 ligase activity.
PTM: Ubiquitinated; undergoes 'Lys-48'-linked autoubiquitination in the absence of growth factors and MAP3K1-induced 'Lys-63'- linked polyubiquitination. 'Lys-48'-autoubiquitination leads to degradation by the proteasome, while MAP3K1-induced 'Lys-63'- linked polyubiquitination results in the stabilization of the protein. 'Lys-48'- and 'Lys-63'-linked polyubiquitinations occur most probably on the same 3 C-terminal lysine residues (Lys-195, Lys-223 and Lys-224) and are thus mutually exclusive. Other sites of ubiquitination are not excluded.
SIMILARITY: Contains 1 RING-type zinc finger.
CAUTION: This sequence initiates at a CTG codon (PubMed:20852630).
SEQUENCE CAUTION: Sequence=AAH12758.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH12758.1; Type=Miscellaneous discrepancy; Note=Unusual initiator. The initiator methionine is coded by a non-canonical CTG leucine codon; Sequence=CAI23328.1; Type=Erroneous gene model prediction;

-  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           more ... click here to view the complete list

+  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: 92.44 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1992.72 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 -49.00125-0.392 Picture PostScript Text
3' UTR -860.742303-0.374 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
IPR018957 - Znf_C3HC4_RING-type
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
PF15227 - zinc finger of C3HC4-type, RING

SCOP Domains:
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q5TA31
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     
      
      
      

-  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

Biological Process:
GO:0008284 positive regulation of cell proliferation
GO:0016567 protein ubiquitination
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045893 positive regulation of transcription, DNA-templated
GO:0051865 protein autoubiquitination
GO:0070936 protein K48-linked ubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LP895165 - Sequence 29 from Patent EP3253886.
BC012758 - Homo sapiens ring finger protein 187, mRNA (cDNA clone IMAGE:3633225), partial cds.
BC064481 - Homo sapiens ring finger protein 187, mRNA (cDNA clone IMAGE:5419471), partial cds.
BC080645 - Homo sapiens ring finger protein 187, mRNA (cDNA clone IMAGE:5093646).
JD322560 - Sequence 303584 from Patent EP1572962.
JD269054 - Sequence 250078 from Patent EP1572962.
JD275961 - Sequence 256985 from Patent EP1572962.
JD469938 - Sequence 450962 from Patent EP1572962.
JD540785 - Sequence 521809 from Patent EP1572962.
JD373286 - Sequence 354310 from Patent EP1572962.
JD203516 - Sequence 184540 from Patent EP1572962.
BC008022 - Homo sapiens ring finger protein 187, mRNA (cDNA clone IMAGE:3538149).
LF209081 - JP 2014500723-A/16584: Polycomb-Associated Non-Coding RNAs.
JD071753 - Sequence 52777 from Patent EP1572962.
JD479599 - Sequence 460623 from Patent EP1572962.
BC000821 - Homo sapiens ring finger protein 187, mRNA (cDNA clone IMAGE:3453993), partial cds.
BC053571 - Homo sapiens ring finger protein 187, mRNA (cDNA clone IMAGE:3861151).
LF325939 - JP 2014500723-A/133442: Polycomb-Associated Non-Coding RNAs.
JD519938 - Sequence 500962 from Patent EP1572962.
JD122928 - Sequence 103952 from Patent EP1572962.
JD376505 - Sequence 357529 from Patent EP1572962.
JD148143 - Sequence 129167 from Patent EP1572962.
JD508715 - Sequence 489739 from Patent EP1572962.
JD338417 - Sequence 319441 from Patent EP1572962.
LF325938 - JP 2014500723-A/133441: Polycomb-Associated Non-Coding RNAs.
JD102305 - Sequence 83329 from Patent EP1572962.
JD071491 - Sequence 52515 from Patent EP1572962.
JD106549 - Sequence 87573 from Patent EP1572962.
JD199037 - Sequence 180061 from Patent EP1572962.
JD311131 - Sequence 292155 from Patent EP1572962.
JD225122 - Sequence 206146 from Patent EP1572962.
JD453485 - Sequence 434509 from Patent EP1572962.
JD469528 - Sequence 450552 from Patent EP1572962.
JD162207 - Sequence 143231 from Patent EP1572962.
JD479250 - Sequence 460274 from Patent EP1572962.
MA561516 - JP 2018138019-A/133442: Polycomb-Associated Non-Coding RNAs.
MA561515 - JP 2018138019-A/133441: Polycomb-Associated Non-Coding RNAs.
MA444658 - JP 2018138019-A/16584: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NL57, NM_001010858, NP_001010858, Q5TA31, Q6P2J7, Q6PJR0, RN187_HUMAN
UCSC ID: uc001htb.3
RefSeq Accession: NM_001010858
Protein: Q5TA31 (aka RN187_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001010858.2
exon count: 4CDS single in 3' UTR: no RNA size: 3133
ORF size: 705CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 962.00frame shift in genome: no % Coverage: 100.00
has start codon: no 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.