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

Gene ID: 23034, updated on 2-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
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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 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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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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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

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