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PXDNL peroxidasin like [ Homo sapiens (human) ]

Gene ID: 137902, updated on 2-Nov-2024

Summary

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Official Symbol
PXDNLprovided by HGNC
Official Full Name
peroxidasin likeprovided by HGNC
Primary source
HGNC:HGNC:26359
See related
Ensembl:ENSG00000147485 MIM:615904; AllianceGenome:HGNC:26359
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
PMR1; PRM1; VPO2
Summary
Predicted to enable heme binding activity and peroxidase activity. Predicted to be involved in hydrogen peroxide catabolic process. Predicted to be located in endoplasmic reticulum; extracellular region; and plasma membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in heart (RPKM 10.6), testis (RPKM 1.5) and 1 other tissue See more
Orthologs
all
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Genomic context

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See PXDNL in Genome Data Viewer
Location:
8q11.22-q11.23
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (51319577..51809445, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (51692630..52185430, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (52232137..52722005, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA7 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:52002970-52003943 Neighboring gene uncharacterized LOC105375831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52117743-52118244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52118245-52118744 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:52243645-52244844 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:52307404-52308603 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:52342412-52342634 Neighboring gene BRIX1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:52446225-52446760 Neighboring gene NANOG hESC enhancer GRCh37_chr8:52631745-52632246 Neighboring gene uncharacterized LOC105375833 Neighboring gene MPRA-validated peak7013 silencer Neighboring gene BTF3 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52721378-52721900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52721901-52722422 Neighboring gene protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27341 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:52837590-52838789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27342 Neighboring gene PCMTD1 divergent transcript

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. PXDNL activates the motility of urothelial bladder carcinoma cells through the Wnt/β-catenin pathway and has a prognostic value. Lu M, et al. Life Sci, 2023 Jan 1. PMID 36493879
  2. Peroxidasins: novel players in tissue genesis. Péterfi Z, et al. Trends Biochem Sci, 2014 Jul. PMID 24924147
  3. Identification of the human PMR1 mRNA endonuclease as an alternatively processed product of the gene for peroxidasin-like protein. Gu SQ, et al. RNA, 2012 Jun. PMID 22543864, Free PMC Article
  4. The PMR1 pump in alpha-synuclein toxicity and neurodegeneration. Nikoletopoulou V, et al. Neurosci Lett, 2018 Jan 10. PMID 28780169
  5. The human PMR1 endonuclease stimulates cell motility by down regulating miR-200 family microRNAs. Gu SQ, et al. Nucleic Acids Res, 2016 Jul 8. PMID 27257068, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PXDNL activates the motility of urothelial bladder carcinoma cells through the Wnt/beta-catenin pathway and has a prognostic value.
    Title: PXDNL activates the motility of urothelial bladder carcinoma cells through the Wnt/β-catenin pathway and has a prognostic value.
  2. We also observe evidence for an excess burden of rare, predicted loss-of-function variation in PXDNL and BMS1- two genes relevant to the broader laterality phenotype. These findings highlight potential new genes in the development of laterality defects, and suggest extensive locus heterogeneity and complex genetic models in this class of birth defects.
    Title: Genetic architecture of laterality defects revealed by whole exome sequencing.
  3. the PMR1 pump, a Golgi resident Ca(2+)/Mn(2+) P-type ATPase, plays a pivotal role in regulating the intracellular levels of calcium and manganese ions.
    Title: The PMR1 pump in alpha-synuclein toxicity and neurodegeneration.
  4. The human PXDN endonuclease stimulates cell motility by down regulating miR-200 family microRNAs.
    Title: The human PMR1 endonuclease stimulates cell motility by down regulating miR-200 family microRNAs.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr Treatment of human primary astrocytes with HIV-1 Vpr upregulates expression of six genes, APOE, CCL5, DGKK, GPX5, NOS2, and PXDNL PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25471

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables endonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables heme binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables lactoperoxidase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables peroxidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables peroxidase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in cellular oxidant detoxification IEA
Inferred from Electronic Annotation
more info
  
involved_in hydrogen peroxide catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in response to oxidative stress IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
probable oxidoreductase PXDNL
Names
cardiac peroxidase
cardiovascular peroxidase 2
inactive peroxidasin-like protein
peroxidasin homolog-like
peroxidasin-like protein
polysomal ribonuclease 1 homolog
vascular peroxidase 2
NP_653252.4
XP_005251225.1
XP_011515760.1
XP_016868530.1
XP_047277320.1
XP_047277321.1
XP_047277322.1
XP_047277323.1
XP_047277325.1
XP_054215729.1
XP_054215730.1
XP_054215731.1
XP_054215732.1
XP_054215733.1
XP_054215734.1
XP_054215735.1
XP_054215736.1

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_144651.5 → NP_653252.4  probable oxidoreductase PXDNL precursor

    Status: VALIDATED

    Source sequence(s)
    AC011128, AC012413, AC090186, AC103958, AC107374
    Consensus CDS
    CCDS47855.1
    UniProtKB/Swiss-Prot
    A1KZ92, B5ME43, B6CGZ3, H0YBM9, Q6ZMR2, Q96LH9
    UniProtKB/TrEMBL
    A0A059U7G5
    Related
    ENSP00000348645.4, ENST00000356297.5
    Conserved Domains (7) summary
    cd09826
    Location:851 → 1286
    peroxidasin_like; Animal heme peroxidase domain of peroxidasin and related proteins
    smart00082
    Location:180 → 232
    LRRCT; Leucine rich repeat C-terminal domain
    smart00214
    Location:1400 → 1450
    VWC; von Willebrand factor (vWF) type C domain
    sd00031
    Location:52 → 85
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:123 → 182
    LRR_8; Leucine rich repeat
    pfam13927
    Location:234 → 309
    Ig_3; Immunoglobulin domain
    cl11960
    Location:528 → 596
    Ig; Immunoglobulin domain

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    51319577..51809445 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047421364.1 → XP_047277320.1  probable oxidoreductase PXDNL isoform X1

  2. XM_047421365.1 → XP_047277321.1  probable oxidoreductase PXDNL isoform X2

  3. XM_047421366.1 → XP_047277322.1  probable oxidoreductase PXDNL isoform X3

  4. XM_047421367.1 → XP_047277323.1  probable oxidoreductase PXDNL isoform X4

  5. XM_011517458.3 → XP_011515760.1  probable oxidoreductase PXDNL isoform X4

    UniProtKB/TrEMBL
    A0A059U7G5
    Conserved Domains (9) summary
    cd09826
    Location:716 → 1151
    peroxidasin_like; Animal heme peroxidase domain of peroxidasin and related proteins
    smart00082
    Location:45 → 97
    LRRCT; Leucine rich repeat C-terminal domain
    smart00214
    Location:1265 → 1315
    VWC; von Willebrand factor (vWF) type C domain
    pfam07679
    Location:377 → 462
    I-set; Immunoglobulin I-set domain
    sd00031
    Location:13 → 36
    LRR_1; leucine-rich repeat [structural motif]
    pfam03098
    Location:592 → 1130
    An_peroxidase; Animal haem peroxidase
    pfam12799
    Location:12 → 47
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:2 → 47
    LRR_8; Leucine rich repeat
    cl11960
    Location:393 → 461
    Ig; Immunoglobulin domain

  6. XM_017013041.2 → XP_016868530.1  probable oxidoreductase PXDNL isoform X4

    UniProtKB/TrEMBL
    A0A059U7G5
    Conserved Domains (9) summary
    cd09826
    Location:716 → 1151
    peroxidasin_like; Animal heme peroxidase domain of peroxidasin and related proteins
    smart00082
    Location:45 → 97
    LRRCT; Leucine rich repeat C-terminal domain
    smart00214
    Location:1265 → 1315
    VWC; von Willebrand factor (vWF) type C domain
    pfam07679
    Location:377 → 462
    I-set; Immunoglobulin I-set domain
    sd00031
    Location:13 → 36
    LRR_1; leucine-rich repeat [structural motif]
    pfam03098
    Location:592 → 1130
    An_peroxidase; Animal haem peroxidase
    pfam12799
    Location:12 → 47
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:2 → 47
    LRR_8; Leucine rich repeat
    cl11960
    Location:393 → 461
    Ig; Immunoglobulin domain

  7. XM_005251168.4 → XP_005251225.1  probable oxidoreductase PXDNL isoform X5

    Conserved Domains (3) summary
    cd09826
    Location:236 → 671
    peroxidasin_like; Animal heme peroxidase domain of peroxidasin and related proteins
    smart00214
    Location:785 → 835
    VWC; von Willebrand factor (vWF) type C domain
    pfam03098
    Location:112 → 650
    An_peroxidase; Animal haem peroxidase

  8. XM_047421369.1 → XP_047277325.1  probable oxidoreductase PXDNL isoform X6

RNA

  1. XR_007060701.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    51692630..52185430 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359754.1 → XP_054215729.1  probable oxidoreductase PXDNL isoform X1

  2. XM_054359755.1 → XP_054215730.1  probable oxidoreductase PXDNL isoform X2

  3. XM_054359756.1 → XP_054215731.1  probable oxidoreductase PXDNL isoform X3

  4. XM_054359757.1 → XP_054215732.1  probable oxidoreductase PXDNL isoform X4

  5. XM_054359758.1 → XP_054215733.1  probable oxidoreductase PXDNL isoform X4

  6. XM_054359759.1 → XP_054215734.1  probable oxidoreductase PXDNL isoform X4

  7. XM_054359760.1 → XP_054215735.1  probable oxidoreductase PXDNL isoform X5

  8. XM_054359761.1 → XP_054215736.1  probable oxidoreductase PXDNL isoform X6

RNA

  1. XR_008487808.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A1KZ92.3 GenPept UniProtKB/Swiss-Prot:A1KZ92

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