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Nrde2 nrde-2 necessary for RNA interference, domain containing [ Mus musculus (house mouse) ]

Gene ID: 217827, updated on 2-Nov-2024

Summary

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Official Symbol
Nrde2provided by MGI
Official Full Name
nrde-2 necessary for RNA interference, domain containingprovided by MGI
Primary source
MGI:MGI:2670969
See related
Ensembl:ENSMUSG00000021179 AllianceGenome:MGI:2670969
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
6720454P05Rik
Summary
Predicted to be involved in several processes, including RNA splicing; positive regulation of RNA export from nucleus; and regulation of gene expression. Predicted to be located in nuclear speck and nucleolus. Orthologous to human NRDE2 (NRDE-2, necessary for RNA interference, domain containing). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thymus adult (RPKM 4.9), CNS E11.5 (RPKM 3.7) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Nrde2 in Genome Data Viewer
Location:
12; 12 E
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (100091709..100126981, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (100125450..100160414, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene malate dehydrogenase 1, NAD (soluble) pseudogene Neighboring gene STARR-positive B cell enhancer mm9_chr12:101348195-101348496 Neighboring gene protease (prosome, macropain) 26S subunit, ATPase 1 Neighboring gene STARR-positive B cell enhancer ABC_E11523 Neighboring gene STARR-positive B cell enhancer ABC_E5350 Neighboring gene STARR-seq mESC enhancer starr_33033 Neighboring gene predicted gene, 36263 Neighboring gene STARR-positive B cell enhancer ABC_E10772 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:101425780-101425963 Neighboring gene predicted gene 10433

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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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Related articles in PubMed

  1. Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. Flemr M, et al. RNA, 2023 Aug. PMID 37137667, Free PMC Article
  2. Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, et al. PLoS Biol, 2003 Dec. PMID 14691545, Free PMC Article
  3. Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. Piao Y, et al. Genome Res, 2001 Sep. PMID 11544199, Free PMC Article
  4. ATG5 is required for B cell polarization and presentation of particulate antigens. Arbogast F, et al. Autophagy, 2019 Feb. PMID 30196744, Free PMC Article
  5. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.
    Title: Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Targeted (1) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in DNA damage response ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA damage response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in RNA splicing ISO
Inferred from Sequence Orthology
more info
  
involved_in RNA splicing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA stabilization ISO
Inferred from Sequence Orthology
more info
  
involved_in mRNA stabilization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
  
involved_in mitotic cell cycle ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of RNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of RNA export from nucleus ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of RNA export from nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulatory ncRNA-mediated heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nuclear speck ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear speck ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
nuclear exosome regulator NRDE2
Names
UPF0614 protein C14orf102 homolog
protein NRDE2 homolog

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_001290303.1 → NP_001277232.1  nuclear exosome regulator NRDE2 isoform a

    See identical proteins and their annotated locations for NP_001277232.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a). The exon combination of this variant is inferred based on tiled partial transcript alignments.
    Source sequence(s)
    AC166349, AW989733, BG067060, BM933283, CD546085, CK619854, CN706272, CN710548, DN174402
    Consensus CDS
    CCDS70414.1
    UniProtKB/Swiss-Prot
    E9QKV8, Q80XC6, Q8R3D7, Q99LT9
    Related
    ENSMUSP00000021596.8, ENSMUST00000021596.9
    Conserved Domains (1) summary
    pfam08424
    Location:322 → 654
    NRDE-2; necessary for RNA interference

  2. NM_001377383.1 → NP_001364312.1  nuclear exosome regulator NRDE2 isoform c

    Status: VALIDATED

    Source sequence(s)
    AC166349
    Conserved Domains (2) summary
    pfam08424
    Location:269 → 601
    NRDE-2; necessary for RNA interference
    cd22200
    Location:142 → 213
    NRDE2_MID; MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins

  3. NM_183155.3 → NP_898978.2  nuclear exosome regulator NRDE2 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a. The exon combination of this variant is inferred based on tiled partial transcript alignments.
    Source sequence(s)
    AC166349, AW989733, BG067060, BM933283, BU055364, CD546085, CK619854, CN706272, CN710548, DN174402
    Conserved Domains (1) summary
    pfam08424
    Location:317 → 649
    NRDE-2; necessary for RNA interference

RNA

  1. NR_165260.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC166349

  2. NR_165261.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC166349

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

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    100091709..100126981 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011244093.4 → XP_011242395.1  nuclear exosome regulator NRDE2 isoform X1

    Conserved Domains (1) summary
    pfam08424
    Location:83 → 415
    NRDE-2; necessary for RNA interference

RNA

  1. XR_381516.5 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80XC6.3 GenPept UniProtKB/Swiss-Prot:Q80XC6

Gene LinkOut

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