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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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See PTRH1 in Genome Data Viewer
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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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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