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    Smndc1 survival motor neuron domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 76479, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Smndc1provided by MGI
    Official Full Name
    survival motor neuron domain containing 1provided by MGI
    Primary source
    MGI:MGI:1923729
    See related
    Ensembl:ENSMUSG00000025024 AllianceGenome:MGI:1923729
    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
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing; apoptotic process; and mRNA processing. Predicted to be located in Cajal body; cytoplasm; and nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Is expressed in brain ventricular layer; genitourinary system; sensory organ; and thymus primordium. Orthologous to human SMNDC1 (survival motor neuron domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in placenta adult (RPKM 8.0), CNS E11.5 (RPKM 7.7) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Smndc1 in Genome Data Viewer
    Location:
    19 D2; 19 47.67 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (53367603..53379065, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (53379214..53390701, complement)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36339 Neighboring gene STARR-seq mESC enhancer starr_46442 Neighboring gene STARR-positive B cell enhancer ABC_E783 Neighboring gene predicted gene, 30541 Neighboring gene MAX interactor 1, dimerization protein Neighboring gene STARR-seq mESC enhancer starr_46448 Neighboring gene VISTA enhancer mm1351 Neighboring gene STARR-positive B cell enhancer ABC_E4292 Neighboring gene STARR-positive B cell enhancer ABC_E1980 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:53499127-53499376 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:53515061-53515299 Neighboring gene STARR-positive B cell enhancer ABC_E5711 Neighboring gene STARR-seq mESC enhancer starr_46454 Neighboring gene RIKEN cDNA 4833407H14 gene Neighboring gene STARR-seq mESC enhancer starr_46456 Neighboring gene myocardial infarction associated transcript 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:53539230-53539416 Neighboring gene predicted gene, 30826

    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. SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression. Casteels T, et al. Cell Rep, 2022 Aug 30. PMID 36044849
    2. An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth. Belleville AE, et al. PLoS Genet, 2024 Aug. PMID 39150991, Free PMC Article
    3. Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR. McAninch DS, et al. Mol Biosyst, 2017 Jul 25. PMID 28612854, Free PMC Article
    4. Positional cloning of Sorcs1, a type 2 diabetes quantitative trait locus. Clee SM, et al. Nat Genet, 2006 Jun. PMID 16682971
    5. Identification and analysis of genes from the mouse otic vesicle and their association with developmental subprocesses through in situ hybridization. Powles N, et al. Dev Biol, 2004 Apr 1. PMID 15031102

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth.
      Title: An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth.
    2. SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression.
      Title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression.
    3. The results show that SMNDC1 mRNA 5'-UTR forms an intramolecular, parallel G quadruplex structure comprised of three G quartet planes, which is bound specifically by FMRP both in vitro and in mouse brain lysates.
      Title: Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    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

    • MGC106917, 2410004J23Rik, 4933440I19Rik

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Cajal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    survival of motor neuron-related-splicing factor 30
    Names
    30 kDa splicing factor SMNrp
    SMN-related protein
    survival motor neuron domain-containing protein 1

    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_001356986.1 → NP_001343915.1  survival of motor neuron-related-splicing factor 30 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC133451, AK077225, AK078834
      Consensus CDS
      CCDS29902.1
      UniProtKB/Swiss-Prot
      Q4QQL0, Q8BGT7
      UniProtKB/TrEMBL
      Q3TGV3
      Related
      ENSMUSP00000157540.2, ENSMUST00000237529.2
      Conserved Domains (1) summary
      pfam06003
      Location:69 → 124
      SMN; Survival motor neuron protein (SMN)

    2. NM_001424870.1 → NP_001411799.1  survival of motor neuron-related-splicing factor 30 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC133451

    3. NM_001424872.1 → NP_001411801.1  survival of motor neuron-related-splicing factor 30 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC133451

    4. NM_172429.3 → NP_766017.1  survival of motor neuron-related-splicing factor 30 isoform 1

      See identical proteins and their annotated locations for NP_766017.1

      Status: VALIDATED

      Description
      Transcript Variant: Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC133451, AK078834, CF750765
      Consensus CDS
      CCDS29902.1
      UniProtKB/Swiss-Prot
      Q4QQL0, Q8BGT7
      UniProtKB/TrEMBL
      Q3TGV3
      Related
      ENSMUSP00000025997.6, ENSMUST00000025997.7
      Conserved Domains (1) summary
      pfam06003
      Location:69 → 124
      SMN; Survival motor neuron protein (SMN)

    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_000085.7 Reference GRCm39 C57BL/6J

      Range
      53367603..53379065 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BGT7.1 GenPept UniProtKB/Swiss-Prot:Q8BGT7

    Gene LinkOut

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