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    PDXDC2P-NPIPB14P PDXDC2P-NPIPB14P readthrough, transcribed pseudogene [ Homo sapiens (human) ]

    Gene ID: 283970, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PDXDC2P-NPIPB14Pprovided by HGNC
    Official Full Name
    PDXDC2P-NPIPB14P readthrough, transcribed pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:53158
    See related
    Ensembl:ENSG00000196696 AllianceGenome:HGNC:53158
    Gene type
    pseudo
    RefSeq status
    PROVISIONAL
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This locus represents naturally-occurring readthrough transcription between two pseudogenes, PDXDC2P (pyridoxal dependent decarboxylase domain containing 2, pseudogene) and NPIPB14P (nuclear pore complex interacting protein family, member B14, pseudogene). The individual pseudogene loci are not curated as transcribed regions. Readthrough transcripts likely do not encode functional proteins. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in testis (RPKM 24.1), duodenum (RPKM 18.2) and 25 other tissues See more
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    Genomic context

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    See PDXDC2P-NPIPB14P in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69976297..70065948, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75785715..75875793, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70010200..70099851, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene WW domain containing E3 ubiquitin protein ligase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:69967565-69967755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:69983944-69984557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:69984558-69985170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69986397-69987010 Neighboring gene microRNA 140 Neighboring gene C-type lectin domain family 18 member A Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70006369-70006869 Neighboring gene MPRA-validated peak2633 silencer Neighboring gene nuclear pore complex interacting protein family member B14, pseudogene Neighboring gene pyridoxal dependent decarboxylase domain containing 2, pseudogene Neighboring gene microRNA 1972-2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70085803-70086756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11048 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70099725-70100338 Neighboring gene uncharacterized LOC124903706 Neighboring gene ribosomal protein S10 pseudogene 24

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Proteome-wide Identification of HtrA2/Omi Substrates. Vande Walle L, et al. J Proteome Res, 2007 Mar. PMID 17266347
    2. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Perry JR, et al. Nature, 2014 Oct 2. PMID 25231870, Free PMC Article
    3. SERBP1 Promotes Stress Granule Clearance by Regulating 26S Proteasome Activity and G3BP1 Ubiquitination and Protects Male Germ Cells from Thermostimuli Damage. Wang F, et al. Research (Wash D C), 2023. PMID 37223481, Free PMC Article
    4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    5. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. Shami Shah A, et al. Cell Rep, 2019 May 14. PMID 31091453, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog

    Variation

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    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

    Other Names

    • PDXDC2P-NPIPB14P readthrough
    • Putative pyridoxal-dependent decarboxylase domain-containing protein 2
    • pyridoxal-dependent decarboxylase domain-containing 2 pseudogene

    Clone Names

    • FLJ23482

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carboxy-lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in carboxylic acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    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.

    RNA

    1. NR_003610.1 RNA Sequence

      Status: PROVISIONAL

      Source sequence(s)
      AL833251
      Related
      ENST00000531894.5

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      69976297..70065948 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      75785715..75875793 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_199134.1: Suppressed sequence

      Description
      NM_199134.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P474.3 GenPept UniProtKB/Swiss-Prot:Q6P474

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials