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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
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Genomic context

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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.

Chemical Information
Molecular Biology Databases
Research Materials
Miscellaneous