Parn poly(A)-specific ribonuclease (deadenylation nuclease) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Parnprovided by MGI
Official Full Name: poly(A)-specific ribonuclease (deadenylation nuclease)provided by MGI
Primary source: MGI:MGI:1921358
See related: Ensembl:ENSMUSG00000022685 AllianceGenome:MGI:1921358
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: DAN; 1200003I18Rik
Summary: Predicted to enable several functions, including poly(A)-specific ribonuclease activity; protein kinase binding activity; and telomerase RNA binding activity. Acts upstream of or within nuclear-transcribed mRNA poly(A) tail shortening. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in glutamatergic synapse; nucleus; and postsynapse. Is expressed in 2-cell stage embryo; central nervous system; and genitourinary system. Human ortholog(s) of this gene implicated in autosomal recessive dyskeratosis congenita 6. Orthologous to human PARN (poly(A)-specific ribonuclease). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in placenta adult (RPKM 9.2), bladder adult (RPKM 7.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A1; 16 9.32 cM

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (13355828..13486035, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (13537964..13668198, complement)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Impaired telomere integrity and rRNA biogenesis in PARN-deficient patients and knock-out models.
Title: Impaired telomere integrity and rRNA biogenesis in PARN-deficient patients and knock-out models.
these data indicate that PARN modulates decay of a defined set of mRNAs in mammalian cells and implicate this deadenylase in coordinating control of genes required for cell movement.
Title: The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts.
poly(A) polymerase Gld2, deadenylase PARN, and translation inhibitory factor neuroguidin (Ngd) are components of a dendritic CPEB-associated polyadenylation apparatus
Title: Bidirectional control of mRNA translation and synaptic plasticity by the cytoplasmic polyadenylation complex.
A modeled PARN, which shows that the RRM domain from one subunit and the R3H domain from the other subunit enclose the active site.
Title: Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease.
Solution structures of the cap-binding domain of mouse PARN with and without the m(7)GpppG cap analog reveal a novel cap-binding mode.
Title: The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation
Gene trapped (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables cation binding	ISO Inferred from Sequence Orthology more info
enables cation binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables poly(A)-specific ribonuclease activity	ISO Inferred from Sequence Orthology more info
enables poly(A)-specific ribonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables telomerase RNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in box H/ACA sno(s)RNA 3'-end processing	ISO Inferred from Sequence Orthology more info
involved_in box H/ACA sno(s)RNA 3'-end processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in miRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in miRNA catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nuclear-transcribed mRNA poly(A) tail shortening	IDA Inferred from Direct Assay more info	PubMed
involved_in poly(A)-dependent snoRNA 3'-end processing	ISO Inferred from Sequence Orthology more info
involved_in poly(A)-dependent snoRNA 3'-end processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of telomere maintenance via telomerase	ISO Inferred from Sequence Orthology more info
involved_in priRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of telomerase RNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
involved_in siRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in telomerase RNA stabilization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: poly(A)-specific ribonuclease PARN

Names: polyadenylate-specific ribonuclease

NP_001345381.1

EC 3.1.13.4

NP_001345382.1

EC 3.1.13.4

NP_083037.1

EC 3.1.13.4

XP_006522715.1

EC 3.1.13.4

XP_017172634.1

EC 3.1.13.4

XP_030105165.1

EC 3.1.13.4

XP_036016049.1

EC 3.1.13.4

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)

NM_001358452.1 → NP_001345381.1 poly(A)-specific ribonuclease PARN isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AC154564, AC154607

UniProtKB/TrEMBL

Q3TUQ8

Conserved Domains (2) summary

pfam08675
Location:412 → 486

RNA_bind; RNA binding domain

pfam04857
Location:3 → 364

CAF1; CAF1 family ribonuclease
NM_001358453.1 → NP_001345382.1 poly(A)-specific ribonuclease PARN isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.

Source sequence(s)

AC154564, AC154607

UniProtKB/TrEMBL

Q3TUQ8

Conserved Domains (2) summary

pfam08675
Location:409 → 483

RNA_bind; RNA binding domain

pfam04857
Location:3 → 361

CAF1; CAF1 family ribonuclease
NM_028761.3 → NP_083037.1 poly(A)-specific ribonuclease PARN isoform 1

See identical proteins and their annotated locations for NP_083037.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC154564, AC154607

Consensus CDS

CCDS37259.1

UniProtKB/TrEMBL

A0A0R4J0P6, Q3TUQ8

Related

ENSMUSP00000055969.9, ENSMUST00000058884.10

Conserved Domains (2) summary

pfam04857
Location:3 → 383

CAF1; CAF1 family ribonuclease

pfam08675
Location:431 → 505

RNA_bind; RNA binding domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

13355828..13486035 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036160156.1 → XP_036016049.1 poly(A)-specific ribonuclease PARN isoform X3

Conserved Domains (2) summary

pfam04857
Location:8 → 190

CAF1; CAF1 family ribonuclease

pfam08675
Location:238 → 312

RNA_bind; RNA binding domain
XM_030249305.2 → XP_030105165.1 poly(A)-specific ribonuclease PARN isoform X1

UniProtKB/TrEMBL

Q3TUQ8

Conserved Domains (3) summary

cd02637
Location:113 → 177

R3H_PARN; R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H ...

pfam04857
Location:192 → 322

CAF1; CAF1 family ribonuclease

pfam08675
Location:370 → 444

RNA_bind; RNA binding domain
XM_017317145.3 → XP_017172634.1 poly(A)-specific ribonuclease PARN isoform X2

UniProtKB/TrEMBL

Q3TUQ8

Conserved Domains (3) summary

cd02637
Location:106 → 155

R3H_PARN; R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H ...

pfam04857
Location:170 → 300

CAF1; CAF1 family ribonuclease

pfam08675
Location:348 → 422

RNA_bind; RNA binding domain
XM_006522652.4 → XP_006522715.1 poly(A)-specific ribonuclease PARN isoform X1

See identical proteins and their annotated locations for XP_006522715.1

UniProtKB/TrEMBL

Q3TUQ8

Conserved Domains (3) summary

cd02637
Location:113 → 177

R3H_PARN; R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H ...

pfam04857
Location:192 → 322

CAF1; CAF1 family ribonuclease

pfam08675
Location:370 → 444

RNA_bind; RNA binding domain