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

Gene ID: 154075, updated on 3-Apr-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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Location:
6q23.1
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (130142752..130365868, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (131337465..131560651, complement)
105.20220307 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 (14) 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)

Genotypes

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_2023_10

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

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