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

Gene ID: 283970, updated on 2-Nov-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: HPA RNA-seq normal tissues 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. 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)

Genotypes

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