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    Snrpn small nuclear ribonucleoprotein N [ Mus musculus (house mouse) ]

    Gene ID: 20646, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Snrpnprovided by MGI
    Official Full Name
    small nuclear ribonucleoprotein Nprovided by MGI
    Primary source
    MGI:MGI:98347
    See related
    Ensembl:ENSMUSG00000102252 AllianceGenome:MGI:98347
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    SMN; Peg4; sm-D; HCERN3; snRNP-N; 2410045I01Rik
    Summary
    This locus represents a paternally-expressed imprinted gene that encodes a component of the small nuclear ribonucleoprotein complex, which functions in pre-mRNA processing. Genomic and genetic changes in this region result in growth defects and lethality; the corresponding region in human is the critical region for Prader-Willi Syndrome. Alternative promoter use and alternative splicing result in a multitude of transcript variants encoding the same protein. Transcript variants may be bicistronic and also encode the SNRPN upstream reading frame protein (Snurf) from an upstream open reading frame. In addition, long spliced transcripts for small nucleolar RNA host gene 14 (Snhg14) may originate from the promoters at this locus and incorporate exons shared with this gene. [provided by RefSeq, Mar 2017]
    Expression
    Biased expression in cerebellum adult (RPKM 199.4), cortex adult (RPKM 198.6) and 8 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Snrpn in Genome Data Viewer
    Location:
    7 B5; 7 34.04 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (59632243..60099925, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (59982495..60450177, complement)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA host gene 14 Neighboring gene small nucleolar RNA, C/D box 107 Neighboring gene small nucleolar RNA, C/D box 64 Neighboring gene SNRPN upstream reading frame Neighboring gene pyruvate dehydrogenase complex, component X pseudogene Neighboring gene 1110014K08Rik pseudogene Neighboring gene predicted gene, 18129 Neighboring gene modulator of retrovirus infection homolog Neighboring gene STARR-seq mESC enhancer starr_18994 Neighboring gene STARR-seq mESC enhancer starr_18995 Neighboring gene sorbitol dehydrogenase pseudogene Neighboring gene G kinase anchoring protein 1 pseudogene Neighboring gene sorbitol dehydrogenase-like

    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
    • 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. Evidence for genetic modifiers of postnatal lethality in PWS-IC deletion mice. Chamberlain SJ, et al. Hum Mol Genet, 2004 Dec 1. PMID 15459179
    2. Behavioural and cognitive abnormalities in an imprinting centre deletion mouse model for Prader-Willi syndrome. Relkovic D, et al. Eur J Neurosci, 2010 Jan. PMID 20092561
    3. A targeted deletion upstream of Snrpn does not result in an imprinting defect. Peery EG, et al. Mamm Genome, 2007 Apr. PMID 17514346
    4. Structure and function correlations at the imprinted mouse Snrpn locus. Gabriel JM, et al. Mamm Genome, 1998 Oct. PMID 9745031
    5. Disruption of imprinted gene methylation and expression in cloned preimplantation stage mouse embryos. Mann MR, et al. Biol Reprod, 2003 Sep. PMID 12748125

    See all (126) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. we found that either knockdown of Nr4a1 or 3, 3'- Diindolylmethane (DIM), an Nr4a1 antagonist, were able to rescue the effects of SNRPN knockdown on neurite outgrowth of embryonic cortical neurons, providing the potential therapeutic methods for SNRPN deletion disorders. We thus concluded that maintaining the proper level of SNRPN is critical in cortical neurodevelopment.
      Title: The autism-related gene SNRPN regulates cortical and spine development via controlling nuclear receptor Nr4a1.
    2. The androgenetic patterns of H19, Snrpn, and Mest were maintained even after differentiation of germline-derived pluripotent stem cells(gPS) into neural stem cells(NSC), whereas the fully unmethylated status of Ndn in SSCs was altered to somatic patterns in gPS cells and gPS-NSCs.
      Title: Epigenetic alteration of imprinted genes during neural differentiation of germline-derived pluripotent stem cells.
    3. These data indicate that oocytes undergo time-dependent demethylation of Snrpn differentially methylated regions during the process of postovulatory aging.
      Title: Loss of methylation imprint of Snrpn in postovulatory aging mouse oocyte.
    4. Oocytes vitrification could lead to the loss of DNA methylation of imprinted genes (H19, Peg3, and Snrpn) in mouse blastocysts, which is mainly caused by the reductions of DNMTs after vitrification of oocytes.
      Title: Effect of oocyte vitrification on deoxyribonucleic acid methylation of H19, Peg3, and Snrpn differentially methylated regions in mouse blastocysts.
    5. These results support a model in which transcription from the Snrpn upstream exons directs the maternal imprint at the PWS-IC
      Title: Transcription is required to establish maternal imprinting at the Prader-Willi syndrome and Angelman syndrome locus.
    6. Snrpn gene is imprinted, with monoallelic expression from the paternal allele in brain and heart.
      Title: Structure of the imprinted mouse Snrpn gene and establishment of its parental-specific methylation pattern.
    7. The tissue-specific methylation of the mouse conserved activator sequence and its methylation-sensitive enhancer activity may control expression of imprinting center transcripts, establishing and/or maintaining imprinting in the Snrpn locus.
      Title: Developmentally dynamic changes of DNA methylation in the mouse Snurf/Snrpn gene.
    8. the ATG-to-AAG mutation causes a 15-fold or more increase in translation of the downstream ORF in two fusion constructs, and it is likely that similar translational control affects the normal Snurf-Snrpn transcript as well
      Title: Evidence for translational regulation of the imprinted Snurf-Snrpn locus in mice.
    9. Mouse model for Prader-Willi syndrome. Deletion of Snrpn gene and putative imprinting-centre is associated with absent expression of the imprinted genes Zfp127, Ndn and Ipw, and phenotypes similar to those found in Prader-Willi infants.
      Title: A mouse model for Prader-Willi syndrome imprinting-centre mutations.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (8)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC18604, MGC30325

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables snRNP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to hormone IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of U1 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U1 snRNP IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of U1 snRNP ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2 snRNP IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of U2 snRNP ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type prespliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U5 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    small nuclear ribonucleoprotein-associated protein N
    Names
    sm protein D
    sm protein N
    tissue-specific-splicing protein

    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_001082961.2 → NP_001076430.1  small nuclear ribonucleoprotein-associated protein N

      See identical proteins and their annotated locations for NP_001076430.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter compared to variant 1.
      Source sequence(s)
      AC172750, AK013607, AK144386, BQ042870, BU708754, BY269658, CB523964
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    2. NM_001082962.2 → NP_001076431.1  small nuclear ribonucleoprotein-associated protein N

      See identical proteins and their annotated locations for NP_001076431.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents use of an alternate promoter compared to variant 1.
      Source sequence(s)
      AC046145, AC172750, AK013607, AK144386, BU614958, BU708754, CB523964
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Related
      ENSMUSP00000096003.4, ENSMUST00000098402.5
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    3. NM_001349690.1 → NP_001336619.1  small nuclear ribonucleoprotein-associated protein N

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents use of an alternate promoter compared to variant 1.
      Source sequence(s)
      AC172750, AK144386, BC072564, CB523964
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    4. NM_001349691.1 → NP_001336620.1  small nuclear ribonucleoprotein-associated protein N

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) represents use of an alternate promoter compared to variant 1.
      Source sequence(s)
      AC046145, AC172750
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    5. NM_001349692.1 → NP_001336621.1  small nuclear ribonucleoprotein-associated protein N

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) represents use of an alternate promoter compared to variant 1.
      Source sequence(s)
      AC046145, AC167813, AC172750
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    6. NM_001349693.1 → NP_001336622.1  small nuclear ribonucleoprotein-associated protein N

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) represents use of an alternate promoter compared to variant 1.
      Source sequence(s)
      AC167813, AC172750
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    7. NM_001349694.1 → NP_001336623.1  small nuclear ribonucleoprotein-associated protein N

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AC167813, AC172750
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    8. NM_001349695.1 → NP_001336624.1  small nuclear ribonucleoprotein-associated protein N

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AC167813, AC172750
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    9. NM_013670.4 → NP_038698.1  small nuclear ribonucleoprotein-associated protein N

      See identical proteins and their annotated locations for NP_038698.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant variant. This splice variant is bicistronic and can also encode the Snurf protein from an upstream open reading frame.
      Source sequence(s)
      AC172750, AK013607, AK144386, BU708754, BY265277, CB523964
      Consensus CDS
      CCDS39974.1
      UniProtKB/Swiss-Prot
      P63163
      UniProtKB/TrEMBL
      O70499, Q3UN87
      Related
      ENSMUSP00000055941.11, ENSMUST00000059305.17
      Conserved Domains (1) summary
      cd01717
      Location:5 → 83
      Sm_B; Sm protein B

    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_000073.7 Reference GRCm39 C57BL/6J

      Range
      59632243..60099925 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P63163.1 GenPept UniProtKB/Swiss-Prot:P63163

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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