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

Gene ID: 20646, updated on 11-Apr-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. Paradoxical leanness in the imprinting-centre deletion mouse model for Prader-Willi syndrome. Golding DM, et al. J Endocrinol, 2017 Jan. PMID 27799465, Free PMC Article
  2. Calorie seeking, but not hedonic response, contributes to hyperphagia in a mouse model for Prader-Willi syndrome. Davies JR, et al. Eur J Neurosci, 2015 Aug. PMID 26040449, Free PMC Article
  3. Regulatory elements associated with paternally-expressed genes in the imprinted murine Angelman/Prader-Willi syndrome domain. Rodriguez-Jato S, et al. PLoS One, 2013. PMID 23390487, Free PMC Article
  4. Temporal and developmental requirements for the Prader-Willi imprinting center. DuBose AJ, et al. Proc Natl Acad Sci U S A, 2012 Feb 28. PMID 22331910, Free PMC Article
  5. Transcription is required to establish maternal imprinting at the Prader-Willi syndrome and Angelman syndrome locus. Smith EY, et al. PLoS Genet, 2011 Dec. PMID 22242001, Free PMC Article

See all (122) 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)
  • Targeted (8)  1 citation
  • Endonuclease-mediated (2) 

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
  
Component Evidence Code Pubs
part_of U1 snRNP IBA
Inferred from Biological aspect of Ancestor
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 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 ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
  

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

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