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PDXP pyridoxal phosphatase [ Homo sapiens (human) ]

Gene ID: 57026, updated on 4-Dec-2022

Summary

Official Symbol
PDXPprovided by HGNC
Official Full Name
pyridoxal phosphataseprovided by HGNC
Primary source
HGNC:HGNC:30259
See related
Ensembl:ENSG00000241360 MIM:609246; AllianceGenome:HGNC:30259
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CIN; PLP; dJ37E16.5
Summary
Pyridoxal 5-prime-phosphate (PLP) is the active form of vitamin B6 that acts as a coenzyme in maintaining biochemical homeostasis. The preferred degradation route from PLP to 4-pyridoxic acid involves the dephosphorylation of PLP by PDXP (Jang et al., 2003 [PubMed 14522954]).[supplied by OMIM, Mar 2008]
Expression
Broad expression in brain (RPKM 43.8), small intestine (RPKM 14.2) and 21 other tissues See more
Orthologs
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Genomic context

See PDXP in Genome Data Viewer
Location:
22q13.1
Exon count:
2
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37658723..37666932)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38120012..38128169)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (38054730..38062939)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene golgi associated, gamma adaptin ear containing, ARF binding protein 1 Neighboring gene SH3 domain binding protein 1 Neighboring gene PDXP divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 385, pseudogene Neighboring gene galectin 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genes linked to energy metabolism and immunoregulatory mechanisms are associated with subcutaneous adipose tissue distribution in HIV-infected men.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: SH3BP1

Homology

Clone Names

  • FLJ32703

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables glycerol-3-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables heat shock protein binding IDA
Inferred from Direct Assay
more info
PubMed 
enables magnesium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
enables phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables phosphoprotein phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables pyridoxal phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables pyridoxal phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell-cell junction IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with cleavage furrow IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with contractile ring IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
located_in lamellipodium membrane IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with midbody IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with ruffle membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
chronophin
Names
PLP phosphatase
pyridoxal (pyridoxine, vitamin B6) phosphatase
pyridoxal phosphate phosphatase
testicular secretory protein Li 36
NP_064711.1

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.

mRNA and Protein(s)

  1. NM_020315.5NP_064711.1  chronophin

    See identical proteins and their annotated locations for NP_064711.1

    Status: VALIDATED

    Source sequence(s)
    BC064922, Z83844
    Consensus CDS
    CCDS13953.1
    UniProtKB/Swiss-Prot
    Q96GD0, Q9UGY2
    UniProtKB/TrEMBL
    A0A024R1I3
    Related
    ENSP00000215904.6, ENST00000215904.7
    Conserved Domains (1) summary
    TIGR01452
    Location:18290
    PGP_euk; phosphoglycolate/pyridoxal phosphate phosphatase family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    37658723..37666932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    38120012..38128169
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)