PXDNL peroxidasin like [Homo sapiens (human)] - Gene

Summary

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

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.

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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)

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

G32126 (e-PCR)
- UniSTS:39194

SHGC-81322 (e-PCR)
- UniSTS:102687

D8S517 (e-PCR), detects polymorphism
- UniSTS:75307

RH121828 (e-PCR)
- UniSTS:134977

RH69838 (e-PCR)
- UniSTS:65345

SHGC-105297 (e-PCR)
- UniSTS:169290

D8S1622 (e-PCR)
- UniSTS:49760

D8S517 (e-PCR), detects polymorphism
- UniSTS:74891

NoName (e-PCR)
- UniSTS:482459

RH36241 (e-PCR)
- UniSTS:6556

D8S1097 (e-PCR)
- UniSTS:149917

RH102382 (e-PCR)
- UniSTS:96716

SHGC-155384 (e-PCR)
- UniSTS:184789

G32150 (e-PCR)
- UniSTS:8683

D8S1773 (e-PCR)
- UniSTS:83181

SHGC-149241 (e-PCR)
- UniSTS:176881

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

EC 1.11.1.7

XP_005251225.1

EC 1.11.1.7

XP_011515760.1

EC 1.11.1.7

XP_016868530.1

EC 1.11.1.7

XP_047277320.1

EC 1.11.1.7

XP_047277321.1

EC 1.11.1.7

XP_047277322.1

EC 1.11.1.7

XP_047277323.1

EC 1.11.1.7

XP_047277325.1

EC 1.11.1.7

XP_054215729.1

EC 1.11.1.7

XP_054215730.1

EC 1.11.1.7

XP_054215731.1

EC 1.11.1.7

XP_054215732.1

EC 1.11.1.7

XP_054215733.1

EC 1.11.1.7

XP_054215734.1

EC 1.11.1.7

XP_054215735.1

EC 1.11.1.7

XP_054215736.1

EC 1.11.1.7

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)

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

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

51319577..51809445 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047421364.1 → XP_047277320.1 probable oxidoreductase PXDNL isoform X1
XM_047421365.1 → XP_047277321.1 probable oxidoreductase PXDNL isoform X2
XM_047421366.1 → XP_047277322.1 probable oxidoreductase PXDNL isoform X3
XM_047421367.1 → XP_047277323.1 probable oxidoreductase PXDNL isoform X4
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
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
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
XM_047421369.1 → XP_047277325.1 probable oxidoreductase PXDNL isoform X6