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

Gene ID: 5073, updated on 8-Dec-2018

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

Genomic context

See PARN in Genome Data Viewer
Location:
16p13.12
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (14435700..14630286, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (14529557..14724128, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8431 Neighboring gene MIR193B host gene Neighboring gene long intergenic non-protein coding RNA 2130 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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from BioSystems

  • ATF4 activates genes, organism-specific biosystem (from REACTOME)
    ATF4 activates genes, organism-specific biosystemATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
  • Deadenylation of mRNA, organism-specific biosystem (from REACTOME)
    Deadenylation of mRNA, organism-specific biosystemDeadenylation of mRNA proceeds in two steps. According to current models, in the first step the poly(A) tail is shortened from about 200 adenosine residues to about 80 residues by the PAN2-PAN3 compl...
  • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
    Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystemKSRP binds to AU-rich sequences in the 3' untranslated regions of mRNAs. KSRP causes the bound mRNA to be targeted for hydrolysis by recruiting exonucleases and decapping enzymes. The activity of KSR...
  • Lung fibrosis, organism-specific biosystem (from WikiPathways)
    Lung fibrosis, organism-specific biosystemLung fibrosis pathway linked to events (molecular initiating event, key events and associative events) in a putative Adverse Outcome Pathway for lung fibrosis.
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • PERK regulates gene expression, organism-specific biosystem (from REACTOME)
    PERK regulates gene expression, organism-specific biosystemPERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintaine...
  • RNA degradation, organism-specific biosystem (from KEGG)
    RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • RNA degradation, conserved biosystem (from KEGG)
    RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystem (from REACTOME)
    Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystemRNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-eleme...
  • Unfolded Protein Response (UPR), organism-specific biosystem (from REACTOME)
    Unfolded Protein Response (UPR), organism-specific biosystemThe Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER d...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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)

mRNA and Protein(s)

  1. NM_001134477.2NP_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, DA308295
    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_001242992.1NP_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, ENST00000437198.6
    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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    14435700..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

    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

    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

    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.p12 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    8557..203127 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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