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    SAMD3 sterile alpha motif domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 154075, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SAMD3provided by HGNC
    Official Full Name
    sterile alpha motif domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:21574
    See related
    Ensembl:ENSG00000164483 MIM:620516; AllianceGenome:HGNC:21574
    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
    Expression
    Broad expression in lymph node (RPKM 2.9), spleen (RPKM 2.8) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAMD3 in Genome Data Viewer
    Location:
    6q23.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (130142752..130365868, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (131337465..131560651, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (130465460..130687013, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377999 Neighboring gene Sharpr-MPRA regulatory region 9310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25051 Neighboring gene transmembrane protein 244 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:130267865-130268391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:130280283-130280819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:130280820-130281355 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130290138-130290858 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130322225-130322782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25053 Neighboring gene L3MBTL histone methyl-lysine binding protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25055 Neighboring gene NANOG hESC enhancer GRCh37_chr6:130473790-130474410 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:130498512-130498711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:130515807-130516307 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130518767-130519347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25059 Neighboring gene uncharacterized LOC112267974 Neighboring gene MPRA-validated peak6122 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17539 Neighboring gene transmembrane protein 200A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25060 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:130838308-130839507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17540 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:130923105-130924304 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:130935046-130936245 Neighboring gene Sharpr-MPRA regulatory region 149 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130953902-130954652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:131022881-131023397 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:131032856-131033370 Neighboring gene uncharacterized LOC105378002 Neighboring gene uncharacterized LOC105378003

    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. Gene-environment interaction in the etiology of mathematical ability using SNP sets. Docherty SJ, et al. Behav Genet, 2011 Jan. PMID 20978832, Free PMC Article
    2. Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans. Jeff JM, et al. Ann Hum Genet, 2013 Jul. PMID 23534349, Free PMC Article
    3. Generalist genes analysis of DNA markers associated with mathematical ability and disability reveals shared influence across ages and abilities. Docherty SJ, et al. BMC Genet, 2010 Jul 5. PMID 20602751, Free PMC Article
    4. Many sequence variants affecting diversity of adult human height. Gudbjartsson DF, et al. Nat Genet, 2008 May. PMID 18391951
    5. A Y2H-seq approach defines the human protein methyltransferase interactome. Weimann M, et al. Nat Methods, 2013 Apr. PMID 23455924

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator)
      Title: Gene-environment interaction in the etiology of mathematical ability using SNP sets.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Generalist genes analysis of DNA markers associated with mathematical ability and disability reveals shared influence across ages and abilities.
    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
    Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    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

    • FLJ34563, MGC35163

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sterile alpha motif domain-containing protein 3
    Names
    SAM domain-containing protein 3

    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_001017373.4 → NP_001017373.2  sterile alpha motif domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001017373.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1. Both variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AI129628, AK091882, AK302228, AL355581
      Consensus CDS
      CCDS34539.1
      UniProtKB/Swiss-Prot
      B4DY20, E1P576, J3KQK4, Q4VXD8, Q8N6K7, Q8NAY1, Q8NB96
      Related
      ENSP00000403565.2, ENST00000439090.7
      Conserved Domains (1) summary
      cd09526
      Location:1 → 66
      SAM_Samd3; SAM domain of Samd3 subfamily

    2. NM_001258275.3 → NP_001245204.1  sterile alpha motif domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001245204.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Both variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AI129628, AK091351, AK091882, AL121947, KF458284
      Consensus CDS
      CCDS34539.1
      UniProtKB/Swiss-Prot
      B4DY20, E1P576, J3KQK4, Q4VXD8, Q8N6K7, Q8NAY1, Q8NB96
      Related
      ENSP00000357116.2, ENST00000368134.6
      Conserved Domains (1) summary
      cd09526
      Location:1 → 66
      SAM_Samd3; SAM domain of Samd3 subfamily

    3. NM_001277185.2 → NP_001264114.1  sterile alpha motif domain-containing protein 3 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate exon structure in the 5' UTR and 5' coding region. These differences cause translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a longer N-terminus compared to isoform 1.
      Source sequence(s)
      AK302228, AL355581
      Consensus CDS
      CCDS64525.1
      UniProtKB/Swiss-Prot
      Q8N6K7
      Related
      ENSP00000402092.2, ENST00000457563.6
      Conserved Domains (2) summary
      cd09526
      Location:25 → 90
      SAM_Samd3; SAM domain of Samd3 subfamily
      smart00454
      Location:25 → 89
      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      130142752..130365868 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418239.1 → XP_047274195.1  sterile alpha motif domain-containing protein 3 isoform X3

      UniProtKB/Swiss-Prot
      B4DY20, E1P576, J3KQK4, Q4VXD8, Q8N6K7, Q8NAY1, Q8NB96

    2. XM_024446335.2 → XP_024302103.1  sterile alpha motif domain-containing protein 3 isoform X3

      UniProtKB/Swiss-Prot
      B4DY20, E1P576, J3KQK4, Q4VXD8, Q8N6K7, Q8NAY1, Q8NB96
      Conserved Domains (1) summary
      cd09526
      Location:1 → 66
      SAM_Samd3; SAM domain of Samd3 subfamily

    3. XM_024446337.2 → XP_024302105.1  sterile alpha motif domain-containing protein 3 isoform X3

      UniProtKB/Swiss-Prot
      B4DY20, E1P576, J3KQK4, Q4VXD8, Q8N6K7, Q8NAY1, Q8NB96
      Conserved Domains (1) summary
      cd09526
      Location:1 → 66
      SAM_Samd3; SAM domain of Samd3 subfamily

    4. XM_017010305.2 → XP_016865794.1  sterile alpha motif domain-containing protein 3 isoform X2

      Conserved Domains (2) summary
      cd09526
      Location:21 → 86
      SAM_Samd3; SAM domain of Samd3 subfamily
      smart00454
      Location:21 → 85
      SAM; Sterile alpha motif

    5. XM_024446333.2 → XP_024302101.1  sterile alpha motif domain-containing protein 3 isoform X1

      Conserved Domains (1) summary
      cd09526
      Location:21 → 86
      SAM_Samd3; SAM domain of Samd3 subfamily

    6. XM_017010308.3 → XP_016865797.2  sterile alpha motif domain-containing protein 3 isoform X4

      Conserved Domains (1) summary
      cl15755
      Location:21 → 86
      SAM_superfamily; SAM (Sterile alpha motif )

    7. XM_017010309.3 → XP_016865798.2  sterile alpha motif domain-containing protein 3 isoform X5

      UniProtKB/TrEMBL
      E9PR28
      Conserved Domains (1) summary
      cl15755
      Location:21 → 86
      SAM_superfamily; SAM (Sterile alpha motif )

    8. XM_017010310.3 → XP_016865799.2  sterile alpha motif domain-containing protein 3 isoform X6

      UniProtKB/TrEMBL
      E9PR28
      Related
      ENSP00000324874.6, ENST00000324172.10
      Conserved Domains (1) summary
      cl15755
      Location:21 → 86
      SAM_superfamily; SAM (Sterile alpha motif )

    RNA

    1. XR_001743174.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      131337465..131560651 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354346.1 → XP_054210321.1  sterile alpha motif domain-containing protein 3 isoform X2

    2. XM_054354347.1 → XP_054210322.1  sterile alpha motif domain-containing protein 3 isoform X3

      UniProtKB/Swiss-Prot
      B4DY20, E1P576, J3KQK4, Q4VXD8, Q8N6K7, Q8NAY1, Q8NB96

    3. XM_054354344.1 → XP_054210319.1  sterile alpha motif domain-containing protein 3 isoform X1

    4. XM_054354343.1 → XP_054210318.1  sterile alpha motif domain-containing protein 3 isoform X1

    5. XM_054354345.1 → XP_054210320.1  sterile alpha motif domain-containing protein 3 isoform X1

    6. XM_054354348.1 → XP_054210323.1  sterile alpha motif domain-containing protein 3 isoform X4

    7. XM_054354349.1 → XP_054210324.1  sterile alpha motif domain-containing protein 3 isoform X5

    8. XM_054354350.1 → XP_054210325.1  sterile alpha motif domain-containing protein 3 isoform X6

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152552.2: Suppressed sequence

      Description
      NM_152552.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N6K7.2 GenPept UniProtKB/Swiss-Prot:Q8N6K7

    Gene LinkOut

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

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