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    PXDNL peroxidasin like [ Homo sapiens (human) ]

    Gene ID: 137902, updated on 10-Dec-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, Dec 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: 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. 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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    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

    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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

    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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

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

      UniProtKB/TrEMBL
      A0A059U7G5

    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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