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    SAMD4A sterile alpha motif domain containing 4A [ Homo sapiens (human) ]

    Gene ID: 23034, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SAMD4Aprovided by HGNC
    Official Full Name
    sterile alpha motif domain containing 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:23023
    See related
    Ensembl:ENSG00000020577 MIM:610747; AllianceGenome:HGNC:23023
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SMG; SMGA; SAMD4; SMAUG; SMAUG1
    Summary
    Sterile alpha motifs (SAMs) in proteins such as SAMD4A are part of an RNA-binding domain that functions as a posttranscriptional regulator by binding to an RNA sequence motif known as the Smaug recognition element, which was named after the Drosophila Smaug protein (Baez and Boccaccio, 2005 [PubMed 16221671]).[supplied by OMIM, Mar 2008]
    Expression
    Broad expression in testis (RPKM 19.6), heart (RPKM 19.4) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAMD4A in Genome Data Viewer
    Location:
    14q22.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (54565316..54793315)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (48771187..48998510)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (55033846..55260033)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5764 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:54976514-54976699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8412 Neighboring gene glia maturation factor beta Neighboring gene cell growth regulator with ring finger domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5772 Neighboring gene uncharacterized LOC112268133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:55116884-55117491 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:55117492-55118098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:55119678-55120414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8414 Neighboring gene SAMD4A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5773 Neighboring gene Sharpr-MPRA regulatory region 12509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8416 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:55239710-55240909 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:55271438-55272239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:55275033-55275533 Neighboring gene Sharpr-MPRA regulatory region 1906 Neighboring gene RNA, U6atac small nuclear 9, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:55337424-55338029 Neighboring gene GTP cyclohydrolase 1 Neighboring gene microRNA 4308

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SAMD4A serves as a negative prognostic marker for gastric cancer patients. Li D, et al. Tissue Cell, 2023 Oct. PMID 37515967
    2. RNA-binding protein SAMD4A inhibits breast tumor angiogenesis by modulating the balance of angiogenesis program. Zhou M, et al. Cancer Sci, 2021 Sep. PMID 34219323, Free PMC Article
    3. 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
    4. Circular RNA SAMD4A controls adipogenesis in obesity through the miR-138-5p/EZH2 axis. Liu Y, et al. Theranostics, 2020. PMID 32292524, Free PMC Article
    5. 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

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SAMD4A serves as a negative prognostic marker for gastric cancer patients.
      Title: SAMD4A serves as a negative prognostic marker for gastric cancer patients.
    2. Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar.
      Title: Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar.
    3. 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.
    4. RNA-binding protein SAMD4A inhibits breast tumor angiogenesis by modulating the balance of angiogenesis program.
      Title: RNA-binding protein SAMD4A inhibits breast tumor angiogenesis by modulating the balance of angiogenesis program.
    5. Circular RNA SAMD4A controls adipogenesis in obesity through the miR-138-5p/EZH2 axis.
      Title: Circular RNA SAMD4A controls adipogenesis in obesity through the miR-138-5p/EZH2 axis.
    6. The Smaug1 is expressed during synaptogenesis, and Smaug1 knockdown affected the number and size of synapses, and also provoked an impaired response to repetitive depolarizing stimuli, as indicated by a reduced induction of Arc/Arg3.1.
      Title: Smaug1 mRNA-silencing foci respond to NMDA and modulate synapse formation.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. 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

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Gene network analysis in a pediatric cohort identifies novel lung function genes.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1053, DKFZp434H0350, DKFZp686A1532

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables translation repressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein Smaug homolog 1
    Names
    SAM domain-containing protein 4A

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001161576.2 → NP_001155048.2  protein Smaug homolog 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AB028976, AK074716, AW129053, BC121174, DA393986
      Consensus CDS
      CCDS55917.2
      UniProtKB/Swiss-Prot
      Q9UPU9
      Related
      ENSP00000251091.5, ENST00000251091.9
      Conserved Domains (2) summary
      cd09557
      Location:238 → 294
      SAM_Smaug; SAM domain of Smaug subfamily
      smart00454
      Location:236 → 295
      SAM; Sterile alpha motif

    2. NM_001161577.2 → NP_001155049.1  protein Smaug homolog 1 isoform 3

      See identical proteins and their annotated locations for NP_001155049.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream start codon, and includes an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AB028976, AL133444, AW129053, BC011489, BC021726
      Consensus CDS
      CCDS55918.1
      UniProtKB/TrEMBL
      G3V2R1, Q8WW19
      Related
      ENSP00000450808.1, ENST00000555192.1

    3. NM_015589.6 → NP_056404.4  protein Smaug homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_056404.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB028976, AK024652, AK074716, AL133444, AL359792, BC121174, DA393986
      Consensus CDS
      CCDS32084.2
      UniProtKB/Swiss-Prot
      A8MPZ5, Q0VA96, Q6PEW4, Q9UPU9
      Related
      ENSP00000452535.1, ENST00000554335.6
      Conserved Domains (2) summary
      cd09557
      Location:320 → 382
      SAM_Smaug; SAM domain of Smaug subfamily
      smart00454
      Location:325 → 383
      SAM; Sterile alpha motif

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      54565316..54793315
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431137.1 → XP_047287093.1  protein Smaug homolog 1 isoform X1

    2. XM_047431136.1 → XP_047287092.1  protein Smaug homolog 1 isoform X1

    3. XM_024449516.2 → XP_024305284.1  protein Smaug homolog 1 isoform X2

      Conserved Domains (1) summary
      cd09557
      Location:320 → 382
      SAM_Smaug; SAM domain of Smaug subfamily

    4. XM_047431138.1 → XP_047287094.1  protein Smaug homolog 1 isoform X3

      UniProtKB/Swiss-Prot
      A8MPZ5, Q0VA96, Q6PEW4, Q9UPU9

    5. XM_047431140.1 → XP_047287096.1  protein Smaug homolog 1 isoform X4

    6. XM_047431143.1 → XP_047287099.1  protein Smaug homolog 1 isoform X6

    7. XM_047431144.1 → XP_047287100.1  protein Smaug homolog 1 isoform X7

    8. XM_024449515.2 → XP_024305283.1  protein Smaug homolog 1 isoform X1

      Conserved Domains (1) summary
      cd09557
      Location:320 → 382
      SAM_Smaug; SAM domain of Smaug subfamily

    9. XM_047431146.1 → XP_047287102.1  protein Smaug homolog 1 isoform X7

    10. XM_024449514.2 → XP_024305282.1  protein Smaug homolog 1 isoform X1

      Conserved Domains (1) summary
      cd09557
      Location:320 → 382
      SAM_Smaug; SAM domain of Smaug subfamily

    11. XM_047431139.1 → XP_047287095.1  protein Smaug homolog 1 isoform X3

      UniProtKB/Swiss-Prot
      A8MPZ5, Q0VA96, Q6PEW4, Q9UPU9
      Related
      ENSP00000375919.3, ENST00000392067.7

    12. XM_047431141.1 → XP_047287097.1  protein Smaug homolog 1 isoform X4

    13. XM_047431145.1 → XP_047287101.1  protein Smaug homolog 1 isoform X7

    14. XM_047431142.1 → XP_047287098.1  protein Smaug homolog 1 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      48771187..48998510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375650.1 → XP_054231625.1  protein Smaug homolog 1 isoform X1

    2. XM_054375652.1 → XP_054231627.1  protein Smaug homolog 1 isoform X3

    3. XM_054375658.1 → XP_054231633.1  protein Smaug homolog 1 isoform X7

    4. XM_054375654.1 → XP_054231629.1  protein Smaug homolog 1 isoform X4

    5. XM_054375656.1 → XP_054231631.1  protein Smaug homolog 1 isoform X6

    6. XM_054375651.1 → XP_054231626.1  protein Smaug homolog 1 isoform X2

    7. XM_054375659.1 → XP_054231634.1  protein Smaug homolog 1 isoform X7

    8. XM_054375649.1 → XP_054231624.1  protein Smaug homolog 1 isoform X1

    9. XM_054375657.1 → XP_054231632.1  protein Smaug homolog 1 isoform X7

    10. XM_054375655.1 → XP_054231630.1  protein Smaug homolog 1 isoform X5

    11. XM_054375653.1 → XP_054231628.1  protein Smaug homolog 1 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPU9.3 GenPept UniProtKB/Swiss-Prot:Q9UPU9

    Gene LinkOut

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

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