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    PARN poly(A)-specific ribonuclease [ Homo sapiens (human) ]

    Gene ID: 5073, updated on 8-Jul-2021

    Summary

    Official Symbol
    PARNprovided by HGNC
    Official Full Name
    poly(A)-specific ribonucleaseprovided by HGNC
    Primary source
    HGNC:HGNC:8609
    See related
    Ensembl:ENSG00000140694 MIM:604212
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DAN; DKCB6; PFBMFT4
    Summary
    The protein encoded by this gene is a 3'-exoribonuclease, with similarity to the RNase D family of 3'-exonucleases. It prefers poly(A) as the substrate, hence, efficiently degrades poly(A) tails of mRNAs. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs. This protein is also involved in silencing of certain maternal mRNAs during oocyte maturation and early embryonic development, as well as in nonsense-mediated decay (NMD) of mRNAs that contain premature stop codons. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.4), testis (RPKM 9.5) and 25 other tissues See more
    Orthologs
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    Genomic context

    See PARN in Genome Data Viewer
    Location:
    16p13.12
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (14435701..14630286, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (14529558..14724117, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2130 Neighboring gene Sharpr-MPRA regulatory region 5329 Neighboring gene uncharacterized LOC105371094 Neighboring gene NFE2L2 motif-containing MPRA enhancer 233 Neighboring gene Sharpr-MPRA regulatory regions 10217 and 14533 Neighboring gene uncharacterized LOC107984865 Neighboring gene RNA, 7SL, cytoplasmic 274, pseudogene Neighboring gene RNA, U7 small nuclear 125 pseudogene Neighboring gene bifunctional apoptosis regulator Neighboring gene phospholipase A2 group X

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Dyskeratosis congenita, autosomal recessive 6
    MedGen: C4225356 OMIM: 616353 GeneReviews: Dyskeratosis Congenita
    Compare labs
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    GeneReviews: Not available
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    GeneReviews: Not available
    Pulmonary fibrosis and/or bone marrow failure, telomere-related, 4
    MedGen: C4225347 OMIM: 616371 GeneReviews: Not available
    Compare labs

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5'-exoribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables cation binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables mRNA 3'-UTR binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclease activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables poly(A)-specific ribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables poly(A)-specific ribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables poly(A)-specific ribonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables telomerase RNA binding IC
    Inferred by Curator
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    poly(A)-specific ribonuclease PARN
    Names
    deadenylating nuclease
    deadenylation nuclease
    polyadenylate-specific ribonuclease
    NP_001127949.1
    NP_001229921.1
    NP_002573.1
    XP_011520812.1
    XP_011520813.1
    XP_011520815.1
    XP_011520816.1
    XP_016878747.1
    XP_016878748.1
    XP_016878749.1
    XP_024306060.1

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_042871.1 RefSeqGene

      Range
      5012..199571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1286

    mRNA and Protein(s)

    1. NM_001134477.3NP_001127949.1  poly(A)-specific ribonuclease PARN isoform 2

      See identical proteins and their annotated locations for NP_001127949.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate donor splice site in the 5' terminal exon compared to transcript variant 1, resulting in translation initiation from an alternate, in-frame downstream AUG and a shorter isoform (2) compared to isoform 1.
      Source sequence(s)
      AK023866, AK293189, BF435512
      Consensus CDS
      CCDS45420.1
      UniProtKB/Swiss-Prot
      O95453
      UniProtKB/TrEMBL
      B3KN69
      Related
      ENSP00000345456.7, ENST00000341484.11
      Conserved Domains (2) summary
      pfam04857
      Location:1329
      CAF1; CAF1 family ribonuclease
      pfam08675
      Location:377451
      RNA_bind; RNA binding domain
    2. NM_001242992.2NP_001229921.1  poly(A)-specific ribonuclease PARN isoform 3

      See identical proteins and their annotated locations for NP_001229921.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses two alternate in-frame splice sites and lacks an alternate exon in the 5' coding region compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AK023866, AK301648, BF435512, DA308295
      Consensus CDS
      CCDS58425.1
      UniProtKB/Swiss-Prot
      O95453
      UniProtKB/TrEMBL
      B3KN69
      Related
      ENSP00000410525.2, ENST00000420015.6
      Conserved Domains (2) summary
      pfam04857
      Location:3344
      CAF1; CAF1 family ribonuclease
      pfam08675
      Location:392466
      RNA_bind; RNA binding domain
    3. NM_002582.4NP_002573.1  poly(A)-specific ribonuclease PARN isoform 1

      See identical proteins and their annotated locations for NP_002573.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK023866, AK315020, BF435512
      Consensus CDS
      CCDS45419.1
      UniProtKB/Swiss-Prot
      O95453
      UniProtKB/TrEMBL
      B3KN69
      Related
      ENSP00000387911.2, ENST00000437198.7
      Conserved Domains (2) summary
      pfam08675
      Location:438512
      RNA_bind; RNA binding domain
      pfam04857
      Location:3390
      CAF1; CAF1 family ribonuclease

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

      Range
      14435701..14630286 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522511.2XP_011520813.1  poly(A)-specific ribonuclease PARN isoform X2

      See identical proteins and their annotated locations for XP_011520813.1

      Related
      ENSP00000499078.1, ENST00000651634.1
      Conserved Domains (2) summary
      pfam04857
      Location:3390
      CAF1; CAF1 family ribonuclease
      pfam08675
      Location:438512
      RNA_bind; RNA binding domain
    2. XM_024450292.1XP_024306060.1  poly(A)-specific ribonuclease PARN isoform X6

      Conserved Domains (2) summary
      pfam08675
      Location:159233
      RNA_bind; RNA binding domain
      pfam04857
      Location:3111
      CAF1; CAF1 family ribonuclease
    3. XM_017023259.2XP_016878748.1  poly(A)-specific ribonuclease PARN isoform X6

      Conserved Domains (2) summary
      pfam08675
      Location:159233
      RNA_bind; RNA binding domain
      pfam04857
      Location:3111
      CAF1; CAF1 family ribonuclease
    4. XM_017023260.1XP_016878749.1  poly(A)-specific ribonuclease PARN isoform X6

      Conserved Domains (2) summary
      pfam08675
      Location:159233
      RNA_bind; RNA binding domain
      pfam04857
      Location:3111
      CAF1; CAF1 family ribonuclease
    5. XM_017023258.2XP_016878747.1  poly(A)-specific ribonuclease PARN isoform X3

    6. XM_011522510.3XP_011520812.1  poly(A)-specific ribonuclease PARN isoform X1

      See identical proteins and their annotated locations for XP_011520812.1

      Related
      ENSP00000498644.1, ENST00000651049.1
      Conserved Domains (2) summary
      pfam04857
      Location:3390
      CAF1; CAF1 family ribonuclease
      pfam08675
      Location:438512
      RNA_bind; RNA binding domain
    7. XM_011522513.2XP_011520815.1  poly(A)-specific ribonuclease PARN isoform X4

      See identical proteins and their annotated locations for XP_011520815.1

      Conserved Domains (2) summary
      pfam04857
      Location:1329
      CAF1; CAF1 family ribonuclease
      pfam08675
      Location:377451
      RNA_bind; RNA binding domain
    8. XM_011522514.2XP_011520816.1  poly(A)-specific ribonuclease PARN isoform X5

      See identical proteins and their annotated locations for XP_011520816.1

      Related
      ENSP00000498898.1, ENST00000652051.1
      Conserved Domains (1) summary
      pfam04857
      Location:3390
      CAF1; CAF1 family ribonuclease

    RNA

    1. XR_001751906.2 RNA Sequence

    2. XR_001751907.2 RNA Sequence

    Reference GRCh38.p13 ALT_REF_LOCI_1

    Genomic

    1. NT_187607.1 Reference GRCh38.p13 ALT_REF_LOCI_1

      Range
      8558..203116 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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