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    PRICKLE3 prickle planar cell polarity protein 3 [ Homo sapiens (human) ]

    Gene ID: 4007, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PRICKLE3provided by HGNC
    Official Full Name
    prickle planar cell polarity protein 3provided by HGNC
    Primary source
    HGNC:HGNC:6645
    See related
    Ensembl:ENSG00000012211 MIM:300111; AllianceGenome:HGNC:6645
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Pk3; LMO6; LOAM; LOAS
    Summary
    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]
    Expression
    Ubiquitous expression in skin (RPKM 16.7), esophagus (RPKM 11.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRICKLE3 in Genome Data Viewer
    Location:
    Xp11.23
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (49174802..49186373, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48586552..48598227, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49031151..49042826, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373195 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 1 Neighboring gene RNA, 7SL, cytoplasmic 262, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49019052-49019751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20837 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49022309-49023254 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 10 Neighboring gene MAGI family member, X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20838 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49032849-49033350 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 11 Neighboring gene proteolipid protein 2 Neighboring gene CRISPRi-FlowFISH-validated GATA1 and PLP2 regulatory element Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29635 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 13 Neighboring gene synaptophysin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20843 Neighboring gene SYP antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:49065732-49066931 Neighboring gene calcium voltage-gated channel subunit alpha1 F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:49086994-49087652

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. PRICKLE3 linked to ATPase biogenesis manifested Leber's hereditary optic neuropathy. Yu J, et al. J Clin Invest, 2020 Sep 1. PMID 32516135, Free PMC Article
    2. Sequence-based exon prediction around the synaptophysin locus reveals a gene-rich area containing novel genes in human proximal Xp. Fisher SE, et al. Genomics, 1997 Oct 15. PMID 9344658
    3. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Hauri S, et al. Mol Syst Biol, 2013. PMID 24366813, Free PMC Article
    4. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Wu C, et al. Proteomics, 2007 Jun. PMID 17474147
    5. HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways. Monda JK, et al. Cell Rep, 2023 May 30. PMID 37167062, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRICKLE3 linked to ATPase biogenesis manifested Leber's hereditary optic neuropathy.
      Title: PRICKLE3 linked to ATPase biogenesis manifested Leber's hereditary optic neuropathy.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Leber optic atrophy, susceptibility to
    MedGen: C1839891 OMIM: 308905 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell projection organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    prickle planar cell polarity protein 3
    Names
    LIM domain only protein 6
    LMO-6
    prickle homolog 3
    prickle-like protein 3
    triple LIM domain protein 6

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_017135.2 RefSeqGene

      Range
      5000..16571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001307979.2 → NP_001294908.1  prickle planar cell polarity protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate 5' exon, contains an alternate 5' terminal exon, and uses a downstream start codon, compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AA524273, AK299407, AK303200, BM981706, DC407811
      Consensus CDS
      CCDS78481.1
      UniProtKB/TrEMBL
      B7Z8D2, H0Y413
      Related
      ENSP00000388599.2, ENST00000453382.5
      Conserved Domains (4) summary
      cd09415
      Location:118 → 176
      LIM1_Prickle; The first LIM domain of Prickle
      cd09418
      Location:181 → 236
      LIM2_Prickle; The second LIM domain of Prickle
      cd09420
      Location:241 → 299
      LIM3_Prickle; The third LIM domain of Prickle
      cd09827
      Location:14 → 110
      PET_Prickle; The PET domain of Prickle

    2. NM_006150.5 → NP_006141.2  prickle planar cell polarity protein 3 isoform 1

      See identical proteins and their annotated locations for NP_006141.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA524273, AK299407, AK303200, BC002468, BC016856, BM981706, BP227957
      Consensus CDS
      CCDS14320.1
      UniProtKB/Swiss-Prot
      B7Z8F2, O43900, O76007, Q53XR5
      UniProtKB/TrEMBL
      B2RBS3, Q6IAE4
      Related
      ENSP00000470248.1, ENST00000599218.6
      Conserved Domains (4) summary
      cd09415
      Location:186 → 244
      LIM1_Prickle; The first LIM domain of Prickle
      cd09418
      Location:249 → 304
      LIM2_Prickle; The second LIM domain of Prickle
      cd09420
      Location:309 → 367
      LIM3_Prickle; The third LIM domain of Prickle
      cd09827
      Location:82 → 178
      PET_Prickle; The PET domain of Prickle

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      49174802..49186373 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      48586552..48598227 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43900.2 GenPept UniProtKB/Swiss-Prot:O43900

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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