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    P3H4 prolyl 3-hydroxylase family member 4 (inactive) [ Homo sapiens (human) ]

    Gene ID: 10609, updated on 10-Dec-2024

    Summary

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    Official Symbol
    P3H4provided by HGNC
    Official Full Name
    prolyl 3-hydroxylase family member 4 (inactive)provided by HGNC
    Primary source
    HGNC:HGNC:16946
    See related
    Ensembl:ENSG00000141696 MIM:617419; AllianceGenome:HGNC:16946
    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
    NO55; SC65; NOL55; LEPREL4
    Summary
    This nucleolar protein was first characterized because it was an autoantigen in cases on interstitial cystitis. The protein, with a predicted molecular weight of 50 kDa, appears to be localized in the particulate compartment of the interphase nucleolus, with a distribution distinct from that of nucleolar protein B23. During mitosis it is associated with chromosomes. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in placenta (RPKM 4.3), thyroid (RPKM 4.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See P3H4 in Genome Data Viewer
    Location:
    17q21.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (41801953..41811949, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (42658495..42669488, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (39958205..39968201, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene huntingtin associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39889784-39890326 Neighboring gene RNA, 7SL, cytoplasmic 399, pseudogene Neighboring gene junction plakoglobin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39927459-39927963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39927964-39928467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39932003-39932506 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:39942255-39942467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39947785-39948448 Neighboring gene CRISPRi-validated cis-regulatory element chr17.2540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39956106-39956612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39956613-39957119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39971057-39971558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39971559-39972058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39974907-39975818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39975819-39976730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39977650-39978248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39978249-39978845 Neighboring gene FKBP prolyl isomerase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8501 Neighboring gene 5'-nucleotidase, cytosolic IIIB Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8502 Neighboring gene kelch like family member 10

    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
    • 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. cDNA cloning and characterization of a novel nucleolar protein. Ochs RL, et al. Mol Biol Cell, 1996 Jul. PMID 8862517, Free PMC Article
    2. Identification of nucleolar protein No55 as a tumour-associated autoantigen in patients with prostate cancer. Fosså A, et al. Br J Cancer, 2000 Sep. PMID 10952778, Free PMC Article
    3. P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma. Jin X, et al. Comput Math Methods Med, 2021. PMID 34257701, Free PMC Article
    4. P3H4 is correlated with clinicopathological features and prognosis in bladder cancer. Li W, et al. World J Surg Oncol, 2018 Oct 15. PMID 30322400, Free PMC Article
    5. Identification and characterization of a new autoimmune protein in membranous nephropathy by immunoscreening of a renal cDNA library. Cavazzini F, et al. PLoS One, 2012. PMID 23144993, Free PMC Article

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer.
      Title: P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer.
    2. P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma.
      Title: P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma.
    3. Knockdown of P3H4 inhibits proliferation and invasion of bladder cancer.
      Title: Knockdown of P3H4 inhibits proliferation and invasion of bladder cancer.
    4. High P3H4 expression is associated with bladder cancer.
      Title: P3H4 is correlated with clinicopathological features and prognosis in bladder cancer.
    5. SC65 protein is identified as an autoimmune target in idiopathic membranous nephropathy.
      Title: Identification and characterization of a new autoimmune protein in membranous nephropathy by immunoscreening of a renal cDNA library.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to collagen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in bone remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in collagen biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in collagen fibril organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in peptidyl-lysine hydroxylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synaptonemal complex assembly TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of catalytic complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in condensed nuclear chromosome TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in synaptonemal complex TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    endoplasmic reticulum protein SC65
    Names
    leprecan-like 4
    leprecan-like protein 4
    nucleolar autoantigen (55kD)
    nucleolar autoantigen No55
    nucleolar autoantigen, 55kDa
    prolyl 3-hydroxylase family member 4 (non-enzymatic)
    synaptonemal complex 65
    synaptonemal complex protein SC65

    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_006455.3 → NP_006446.1  endoplasmic reticulum protein SC65 precursor

      See identical proteins and their annotated locations for NP_006446.1

      Status: VALIDATED

      Source sequence(s)
      AK056085, BC007942, U47621
      Consensus CDS
      CCDS11408.1
      UniProtKB/Swiss-Prot
      Q53GI6, Q92791, Q9H4F6
      UniProtKB/TrEMBL
      B4DVZ5
      Related
      ENSP00000377505.1, ENST00000393928.6

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      41801953..41811949 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721640.5 → XP_006721703.2  endoplasmic reticulum protein SC65 isoform X2

      UniProtKB/TrEMBL
      B4DVZ5

    2. XM_047435138.1 → XP_047291094.1  endoplasmic reticulum protein SC65 isoform X1

    3. XM_047435137.1 → XP_047291093.1  endoplasmic reticulum protein SC65 isoform X3

      UniProtKB/TrEMBL
      B4DVZ5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      42658495..42669488 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314726.1 → XP_054170701.1  endoplasmic reticulum protein SC65 isoform X5

      UniProtKB/TrEMBL
      B4DVZ5

    2. XM_054314724.1 → XP_054170699.1  endoplasmic reticulum protein SC65 isoform X4

    3. XM_054314725.1 → XP_054170700.1  endoplasmic reticulum protein SC65 isoform X2

      UniProtKB/TrEMBL
      B4DVZ5

    4. XM_054314723.1 → XP_054170698.1  endoplasmic reticulum protein SC65 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92791.1 GenPept UniProtKB/Swiss-Prot:Q92791

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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