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    PTRH1 peptidyl-tRNA hydrolase 1 homolog [ Homo sapiens (human) ]

    Gene ID: 138428, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PTRH1provided by HGNC
    Official Full Name
    peptidyl-tRNA hydrolase 1 homologprovided by HGNC
    Primary source
    HGNC:HGNC:27039
    See related
    Ensembl:ENSG00000187024 AllianceGenome:HGNC:27039
    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
    PTH1; C9orf115
    Summary
    Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in kidney (RPKM 2.9), testis (RPKM 2.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    9q34.11
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127694150..127715676, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139901102..139922631, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130475942..130477955, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130360792-130361311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130370589-130371088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20307 Neighboring gene syntaxin binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130395219-130396018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29044 Neighboring gene VISTA enhancer hs2342 Neighboring gene OCT4 hESC enhancer GRCh37_chr9:130463106-130463614 Neighboring gene microRNA 3911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130476687-130477343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29047 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130478240-130478416 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130480462-130480664 Neighboring gene cilia and flagella associated protein 157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130488893-130489394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130496147-130497053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20308 Neighboring gene tetratricopeptide repeat domain 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130504225-130504852 Neighboring gene torsin family 2 member A Neighboring gene SH2 domain containing 3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130523547-130524424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130524425-130525300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130526508-130527090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20309 Neighboring gene uncharacterized LOC107987132 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130539526-130539796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29049

    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. Release of Ubiquitinated and Non-ubiquitinated Nascent Chains from Stalled Mammalian Ribosomal Complexes by ANKZF1 and Ptrh1. Kuroha K, et al. Mol Cell, 2018 Oct 18. PMID 30244831, Free PMC Article
    2. Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity. De Pereda JM, et al. J Biol Chem, 2004 Feb 27. PMID 14660562
    3. Protein microarray analysis identifies human cellular prion protein interactors. Satoh J, et al. Neuropathol Appl Neurobiol, 2009 Feb. PMID 18482256
    4. UBE2O and USP7 co-regulate RECQL4 ubiquitinylation and homologous recombination-mediated DNA repair. Huang Q, et al. FASEB J, 2022 Jan. PMID 34921745
    5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. Hendrickson SL, et al. PLoS One, 2010 Sep 21. PMID 20877624, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    2. arrangement of secondary structure elements generates a fold not previously reported for peptidyl-trna hydrolase and intermolecular contacts in the crystal asymmetric unit cell suggest a likely surface for protein-protein interactions
      Title: Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC51999

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables aminoacyl-tRNA hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables aminoacyl-tRNA hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in rescue of stalled ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peptidyl-tRNA hydrolase
    Names
    PTH
    probable peptidyl-tRNA hydrolase
    NP_001002913.1
    NP_001332906.1
    NP_001332907.1
    NP_001332908.1
    NP_001332909.1
    XP_047278730.1
    XP_047278731.1
    XP_054217962.1
    XP_054217963.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001002913.3 → NP_001002913.1  peptidyl-tRNA hydrolase isoform 1

      See identical proteins and their annotated locations for NP_001002913.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC047012, BQ045289, DB141384
      Consensus CDS
      CCDS35147.1
      UniProtKB/Swiss-Prot
      Q86Y79
      Related
      ENSP00000439469.1, ENST00000543175.5
      Conserved Domains (1) summary
      cd00462
      Location:32 → 203
      PTH; Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through ...

    2. NM_001345977.1 → NP_001332906.1  peptidyl-tRNA hydrolase isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AV709373, BC015230, BQ045289, DB141384
      UniProtKB/TrEMBL
      A0A096LP22
      Related
      ENSP00000485347.1, ENST00000456267.5

    3. NM_001345978.1 → NP_001332907.1  peptidyl-tRNA hydrolase isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL162426
      Consensus CDS
      CCDS87693.1
      UniProtKB/TrEMBL
      A0A096LPA3, C9J7Z1
      Related
      ENSP00000418219.1, ENST00000423807.5

    4. NM_001345979.1 → NP_001332908.1  peptidyl-tRNA hydrolase isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC015230, BM691270, BQ045289, DB141384
      UniProtKB/TrEMBL
      A0A096LPA3
      Related
      ENSP00000485479.1, ENST00000414832.2

    5. NM_001345980.1 → NP_001332909.1  peptidyl-tRNA hydrolase isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two alternate coding exons compared to variant 1, that causes a frameshift. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC015230, BE295757, BQ045289, DB141384

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      127694150..127715676 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422774.1 → XP_047278730.1  peptidyl-tRNA hydrolase isoform X1

    2. XM_047422775.1 → XP_047278731.1  peptidyl-tRNA hydrolase isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      139901102..139922631 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361987.1 → XP_054217962.1  peptidyl-tRNA hydrolase isoform X1

    2. XM_054361988.1 → XP_054217963.1  peptidyl-tRNA hydrolase isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86Y79.1 GenPept UniProtKB/Swiss-Prot:Q86Y79

    Gene LinkOut

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

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