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    Samd4 sterile alpha motif domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 74480, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Samd4provided by MGI
    Official Full Name
    sterile alpha motif domain containing 4provided by MGI
    Primary source
    MGI:MGI:1921730
    See related
    Ensembl:ENSMUSG00000021838 AllianceGenome:MGI:1921730
    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
    sunk; Smaug; Samd4a; Smaug1; 1700024G08Rik; 1700111L17Rik; 4933436G17Rik
    Summary
    Predicted to enable mRNA binding activity and translation repressor activity. Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Predicted to act upstream of or within positive regulation of translation. Located in synapse. Is expressed in cerebral cortex and telencephalon. Orthologous to human SAMD4A (sterile alpha motif domain containing 4A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis adult (RPKM 72.9), bladder adult (RPKM 9.4) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    14 C1; 14 24.41 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (47120414..47343274)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (46882965..47105817)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5430 Neighboring gene cell growth regulator with ring finger domain 1 Neighboring gene predicted gene, 34934 Neighboring gene STARR-seq mESC enhancer starr_36564 Neighboring gene predicted gene, 52120 Neighboring gene microRNA 378c Neighboring gene STARR-seq mESC enhancer starr_36566 Neighboring gene predicted gene, 52121 Neighboring gene predicted gene 10371 Neighboring gene predicted gene, 52169 Neighboring gene STARR-positive B cell enhancer ABC_E4106 Neighboring gene GTP cyclohydrolase 1 Neighboring gene poly(A) binding protein, cytoplasmic 2 pseudogene

    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. circSAMD4A participates in the apoptosis and autophagy of dopaminergic neurons via the miR‑29c‑3p‑mediated AMPK/mTOR pathway in Parkinson's disease. Wang W, et al. Mol Med Rep, 2021 Jul. PMID 34080649, Free PMC Article
    2. Mutation of mouse Samd4 causes leanness, myopathy, uncoupled mitochondrial respiration, and dysregulated mTORC1 signaling. Chen Z, et al. Proc Natl Acad Sci U S A, 2014 May 20. PMID 24799716, Free PMC Article
    3. Smaug1 mRNA-silencing foci respond to NMDA and modulate synapse formation. Baez MV, et al. J Cell Biol, 2011 Dec 26. PMID 22201125, Free PMC Article
    4. Mammalian Smaug is a translational repressor that forms cytoplasmic foci similar to stress granules. Baez MV, et al. J Biol Chem, 2005 Dec 30. PMID 16221671
    5. Staufen 1 is expressed by neural precursor cells in the developing murine cortex but is dispensable for NPC self-renewal and neuronal differentiation in vitro. Kuc CA, et al. Brain Res, 2021 Dec 15. PMID 34678304

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. circSAMD4A participates in the apoptosis and autophagy of dopaminergic neurons via the miR29c3pmediated AMPK/mTOR pathway in Parkinson's disease.
      Title: circSAMD4A participates in the apoptosis and autophagy of dopaminergic neurons via the miR‑29c‑3p‑mediated AMPK/mTOR pathway in Parkinson's disease.
    2. Samd4 has a role in leanness, myopathy, uncoupled mitochondrial respiration, and regulation of mTORC1 signaling
      Title: Mutation of mouse Samd4 causes leanness, myopathy, uncoupled mitochondrial respiration, and dysregulated mTORC1 signaling.
    3. Smaug 1 has a role in RNA granule formation and translation regulation in neurons
      Title: Mammalian Smaug is a translational repressor that forms cytoplasmic foci similar to stress granules.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Spontaneous (1) 
    • Chemically induced (ENU) (1)  1 citation
    • Endonuclease-mediated (2) 

    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 RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables translation repressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of translation 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 positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of mRNA stability IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein Smaug homolog 1
    Names
    smaug 1
    sterile alpha motif domain-containing protein 4A

    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_001037221.2 → NP_001032298.1  protein Smaug homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_001032298.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC131586, AC159006, AK134243
      Consensus CDS
      CCDS26982.1
      UniProtKB/Swiss-Prot
      A6H6C5, Q2VA55, Q3TQA5, Q3TTN7, Q3UZ00, Q8CBY1, Q9D3T3
      Related
      ENSMUSP00000022386.9, ENSMUST00000022386.15
      Conserved Domains (1) summary
      cd09557
      Location:320 → 382
      SAM_Smaug; SAM domain of Smaug subfamily

    2. NM_001163433.1 → NP_001156905.1  protein Smaug homolog 1 isoform 3

      See identical proteins and their annotated locations for NP_001156905.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC159006, AK006299, AK161277
      Consensus CDS
      CCDS49468.1
      UniProtKB/TrEMBL
      A0A2D0VMX2, A0A2I3BPM7
      Related
      ENSMUSP00000122833.2, ENSMUST00000125113.9
      Conserved Domains (1) summary
      cd09557
      Location:219 → 281
      SAM_Smaug; SAM domain of Smaug subfamily

    3. NM_001310544.1 → NP_001297473.1  protein Smaug homolog 1 isoform 4

      See identical proteins and their annotated locations for NP_001297473.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AC159006, AK017081, AK133470, AK135279, AV240840, BM939644
      Consensus CDS
      CCDS79301.1
      UniProtKB/Swiss-Prot
      Q8CBY1
      Related
      ENSMUSP00000115569.2, ENSMUST00000125688.2

    4. NM_028966.3 → NP_083242.1  protein Smaug homolog 1 isoform 2

      See identical proteins and their annotated locations for NP_083242.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC131586, AC159006, AK133470, BC145827
      Consensus CDS
      CCDS26983.1
      UniProtKB/TrEMBL
      A0A2I3BPM7
      Related
      ENSMUSP00000098237.4, ENSMUST00000100672.11
      Conserved Domains (1) summary
      cd09557
      Location:238 → 294
      SAM_Smaug; SAM domain of Smaug subfamily

    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_000080.7 Reference GRCm39 C57BL/6J

      Range
      47120414..47343274
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036158884.1 → XP_036014777.1  protein Smaug homolog 1 isoform X2

      UniProtKB/Swiss-Prot
      A6H6C5, Q2VA55, Q3TQA5, Q3TTN7, Q3UZ00, Q8CBY1, Q9D3T3
      Conserved Domains (1) summary
      cd09557
      Location:320 → 382
      SAM_Smaug; SAM domain of Smaug subfamily

    2. XM_030248082.2 → XP_030103942.1  protein Smaug homolog 1 isoform X4

      UniProtKB/TrEMBL
      A0A2I3BPM7
      Related
      ENSMUSP00000114621.2, ENSMUST00000137543.9
      Conserved Domains (1) summary
      cd09557
      Location:238 → 294
      SAM_Smaug; SAM domain of Smaug subfamily

    3. XM_036158883.1 → XP_036014776.1  protein Smaug homolog 1 isoform X1

      Conserved Domains (1) summary
      cd09557
      Location:370 → 432
      SAM_Smaug; SAM domain of Smaug subfamily

    4. XM_006519627.4 → XP_006519690.1  protein Smaug homolog 1 isoform X1

      Conserved Domains (1) summary
      cd09557
      Location:370 → 432
      SAM_Smaug; SAM domain of Smaug subfamily

    5. XM_006519628.3 → XP_006519691.1  protein Smaug homolog 1 isoform X3

      Conserved Domains (1) summary
      cd09557
      Location:269 → 331
      SAM_Smaug; SAM domain of Smaug subfamily

    6. XM_006519631.5 → XP_006519694.1  protein Smaug homolog 1 isoform X5

      See identical proteins and their annotated locations for XP_006519694.1

      UniProtKB/Swiss-Prot
      Q8CBY1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CBY1.2 GenPept UniProtKB/Swiss-Prot:Q8CBY1

    Gene LinkOut

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

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