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    SAMD1 sterile alpha motif domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 90378, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SAMD1provided by HGNC
    Official Full Name
    sterile alpha motif domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:17958
    See related
    Ensembl:ENSG00000141858 MIM:620206; AllianceGenome:HGNC:17958
    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
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be located in cytoplasm and extracellular region. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Ubiquitous expression in colon (RPKM 8.2), brain (RPKM 8.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAMD1 in Genome Data Viewer
    Location:
    19p13.12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (14087851..14090751, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14214143..14217618, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14198663..14201563, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14184754-14185274 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:14185989-14186224 Neighboring gene microRNA 1199 Neighboring gene MISP family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14154 Neighboring gene chromosome 19 open reading frame 67 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14199415-14199924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10230 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10231 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10232 Neighboring gene MPRA-validated peak3379 silencer Neighboring gene protein kinase cAMP-activated catalytic subunit alpha Neighboring gene Sharpr-MPRA regulatory region 14201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14223743-14224430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10233 Neighboring gene small integral membrane protein 46 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10234 Neighboring gene uncharacterized LOC124904642 Neighboring gene anti-silencing function 1B histone chaperone

    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. Atherin: a newly identified, lesion-specific, LDL-binding protein in human atherosclerosis. Lees AM, et al. Atherosclerosis, 2005 Oct. PMID 16159594
    2. The miR-378c-Samd1 circuit promotes phenotypic modulation of vascular smooth muscle cells and foam cells formation in atherosclerosis lesions. Tian S, et al. Sci Rep, 2021 May 18. PMID 34006929, Free PMC Article
    3. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Stielow B, et al. Sci Adv, 2021 May. PMID 33980486, Free PMC Article
    4. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Krönke J, et al. Science, 2014 Jan 17. PMID 24292625, Free PMC Article
    5. Quantitative Proteomics of the SMAD (Suppressor of Mothers against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor SMAD-specific Importin. Baas R, et al. J Biol Chem, 2016 Nov 11. PMID 27703004, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SAMD1 attenuates antiphospholipid syndrome-induced pregnancy complications.
      Title: SAMD1 attenuates antiphospholipid syndrome-induced pregnancy complications.
    2. The miR-378c-Samd1 circuit promotes phenotypic modulation of vascular smooth muscle cells and foam cells formation in atherosclerosis lesions.
      Title: The miR-378c-Samd1 circuit promotes phenotypic modulation of vascular smooth muscle cells and foam cells formation in atherosclerosis lesions.
    3. The nuclear importin IPO5 was identified as a novel interacting protein of SMAD1. Overexpression of IPO5 in various cell lines specifically increases nuclear localization of BMP receptor-activated SMADs (R-SMADs) confirming a functional relationship between IPO5 and BMP but not TGF-beta R-SMADs.
      Title: Quantitative Proteomics of the SMAD (Suppressor of Mothers against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor SMAD-specific Importin.
    4. atherin is present only in atherosclerotic lesions, not in normal intima
      Title: Atherin: a newly identified, lesion-specific, LDL-binding protein in human atherosclerosis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables low-density lipoprotein particle binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in foam cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lipoprotein lipid oxidation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein homooligomerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA methylation-dependent heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sterile alpha motif domain-containing protein 1
    Names
    SAM domain containing 1
    atherin

    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_138352.3 → NP_612361.1  sterile alpha motif domain-containing protein 1

      See identical proteins and their annotated locations for NP_612361.1

      Status: VALIDATED

      Source sequence(s)
      AC022098, AY453840, BC065477
      UniProtKB/Swiss-Prot
      Q6P0R3, Q6PIS7, Q6SPF0, Q96IM4
      UniProtKB/TrEMBL
      E9PIW9
      Related
      ENSP00000431971.2, ENST00000533683.7
      Conserved Domains (2) summary
      cd09583
      Location:459 → 527
      SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily
      smart00454
      Location:459 → 525
      SAM; Sterile alpha motif

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      14087851..14090751 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160022.1 Reference GRCh38.p14 PATCHES

      Range
      299692..303167 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332733.1 → XP_054188708.1  sterile alpha motif domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q6P0R3, Q6PIS7, Q6SPF0, Q96IM4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      14214143..14217618 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322551.1 → XP_054178526.1  sterile alpha motif domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q6P0R3, Q6PIS7, Q6SPF0, Q96IM4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6SPF0.1 GenPept UniProtKB/Swiss-Prot:Q6SPF0

    Gene LinkOut

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

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