Human Gene PRICKLE3 (uc004dmy.1)
  Description: Homo sapiens prickle homolog 3 (Drosophila) (PRICKLE3), mRNA.
RefSeq Summary (NM_006150): LIM domain only 6 is a three LIM domain-containing protein. The LIM domain is a cysteine-rich sequence motif that binds zinc atoms to form a specific protein-binding interface for protein-protein interactions. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chrX:49,031,906-49,042,776 Size: 10,871 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chrX:49,032,022-49,042,750 Size: 10,729 Coding Exon Count: 9 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:49,031,906-49,042,776)mRNA (may differ from genome)Protein (615 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PRIC3_HUMAN
DESCRIPTION: RecName: Full=Prickle-like protein 3; AltName: Full=LIM domain only protein 6; Short=LMO-6; AltName: Full=Triple LIM domain protein 6;
INTERACTION: P00519:ABL1; NbExp=2; IntAct=EBI-1751761, EBI-375543; P06241:FYN; NbExp=2; IntAct=EBI-1751761, EBI-515315;
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the prickle / espinas / testin family.
SIMILARITY: Contains 3 LIM zinc-binding domains.
SIMILARITY: Contains 1 PET domain.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PRICKLE3
Diseases sorted by gene-association score: aland island eye disease (8), congenital stationary night blindness (1)

-  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: 6.94 RPKM in Esophagus - Mucosa
Total median expression: 152.19 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 -9.3026-0.358 Picture PostScript Text
3' UTR -29.40116-0.253 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
IPR010442 - PET_domain
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain
PF06297 - PET Domain

SCOP Domains:
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on O43900
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:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0007275 multicellular organism development
GO:0008150 biological_process
GO:0030030 cell projection organization

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005886 plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  LF211398 - JP 2014500723-A/18901: Polycomb-Associated Non-Coding RNAs.
AK303308 - Homo sapiens cDNA FLJ50430 complete cds, highly similar to LIM domain only protein 6.
AK299407 - Homo sapiens cDNA FLJ50633 complete cds, highly similar to LIM domain only protein 6.
AK303200 - Homo sapiens cDNA FLJ53948 complete cds, highly similar to LIM domain only protein 6.
BC002468 - Homo sapiens prickle homolog 3 (Drosophila), mRNA (cDNA clone MGC:1924 IMAGE:3347651), complete cds.
AK300866 - Homo sapiens cDNA FLJ50698 complete cds, highly similar to LIM domain only protein 6.
BC016856 - Homo sapiens prickle homolog 3 (Drosophila), mRNA (cDNA clone MGC:17145 IMAGE:3846372), complete cds.
AJ011654 - Homo sapiens mRNA for triple LIM domain protein.
JD447524 - Sequence 428548 from Patent EP1572962.
JD213812 - Sequence 194836 from Patent EP1572962.
JD498059 - Sequence 479083 from Patent EP1572962.
AK314788 - Homo sapiens cDNA, FLJ95658, highly similar to Homo sapiens LIM domain only 6 (LMO6), mRNA.
KJ897139 - Synthetic construct Homo sapiens clone ccsbBroadEn_06533 PRICKLE3 gene, encodes complete protein.
BT007423 - Homo sapiens LIM domain only 6 mRNA, complete cds.
CR457211 - Homo sapiens full open reading frame cDNA clone RZPDo834A0921D for gene LMO6, LIM domain only 6; complete cds, incl. stopcodon.
DQ891474 - Synthetic construct clone IMAGE:100004104; FLH177305.01X; RZPDo839G01124D LIM domain only 6 (LMO6) gene, encodes complete protein.
DQ894662 - Synthetic construct Homo sapiens clone IMAGE:100009122; FLH177302.01L; RZPDo839G01123D LIM domain only 6 (LMO6) gene, encodes complete protein.
AB464065 - Synthetic construct DNA, clone: pF1KB7840, Homo sapiens LMO6 gene for prickle homolog 3, without stop codon, in Flexi system.
LF379028 - JP 2014500723-A/186531: Polycomb-Associated Non-Coding RNAs.
MA446975 - JP 2018138019-A/18901: Polycomb-Associated Non-Coding RNAs.
MA614605 - JP 2018138019-A/186531: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: LMO6, NM_006150, NP_006141, O43900, O76007, PRIC3_HUMAN, Q53XR5
UCSC ID: uc004dmy.1
RefSeq Accession: NM_006150
Protein: O43900 (aka PRIC3_HUMAN)
CCDS: CCDS14320.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006150.3
exon count: 9CDS single in 3' UTR: no RNA size: 1990
ORF size: 1848CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3893.00frame 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.