Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SAMD1 Gene

Aliases for SAMD1 Gene

  • Sterile Alpha Motif Domain Containing 1 2 3 5
  • Sterile Alpha Motif Domain-Containing Protein 1 3 4
  • SAM Domain-Containing Protein 1 4
  • SAM Domain Containing 1 3
  • Atherin 3

External Ids for SAMD1 Gene

Previous GeneCards Identifiers for SAMD1 Gene

  • GC19U990301
  • GC19M014062
  • GC19M014199

Summaries for SAMD1 Gene

GeneCards Summary for SAMD1 Gene

SAMD1 (Sterile Alpha Motif Domain Containing 1) is a Protein Coding gene. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is SAMD13.

UniProtKB/Swiss-Prot for SAMD1 Gene

  • May play a role in atherogenesis by immobilizing LDL in the atherial wall.

Additional gene information for SAMD1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SAMD1 Gene

Genomics for SAMD1 Gene

Regulatory Elements for SAMD1 Gene

Enhancers for SAMD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H014089 1.3 ENCODE dbSUPER 0.7 0.0 -35 3 PKNOX1 ARNT ARID4B SIN3A ZBTB7B SLC30A9 ZNF143 ZNF207 SP3 SMARCB1 SAMD1 GC19M014096
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SAMD1 on UCSC Golden Path with GeneCards custom track

Promoters for SAMD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000107489 236 2801 PKNOX1 ARNT ARID4B SIN3A ZBTB7B SLC30A9 ZNF143 ZNF207 JUNB REST

Genomic Location for SAMD1 Gene

Chromosome:
19
Start:
14,087,840 bp from pter
End:
14,091,036 bp from pter
Size:
3,197 bases
Orientation:
Minus strand

Genomic View for SAMD1 Gene

Genes around SAMD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SAMD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SAMD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SAMD1 Gene

Proteins for SAMD1 Gene

  • Protein details for SAMD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6SPF0-SAMD1_HUMAN
    Recommended name:
    Atherin
    Protein Accession:
    Q6SPF0
    Secondary Accessions:
    • Q6P0R3
    • Q6PIS7
    • Q96IM4

    Protein attributes for SAMD1 Gene

    Size:
    538 amino acids
    Molecular mass:
    56052 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SAMD1 Gene

Post-translational modifications for SAMD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SAMD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SAMD1 Gene

Domains & Families for SAMD1 Gene

Gene Families for SAMD1 Gene

Protein Domains for SAMD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SAMD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SAMD1: view

No data available for UniProtKB/Swiss-Prot for SAMD1 Gene

Function for SAMD1 Gene

Molecular function for SAMD1 Gene

UniProtKB/Swiss-Prot Function:
May play a role in atherogenesis by immobilizing LDL in the atherial wall.

Phenotypes for SAMD1 Gene

genes like me logo Genes that share phenotypes with SAMD1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SAMD1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SAMD1 Gene

Localization for SAMD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SAMD1 Gene

Cytoplasm. Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SAMD1 gene
Compartment Confidence
extracellular 3
nucleus 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SAMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SAMD1: view

Pathways & Interactions for SAMD1 Gene

SuperPathways for SAMD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SAMD1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SAMD1 Gene

Drugs & Compounds for SAMD1 Gene

No Compound Related Data Available

Transcripts for SAMD1 Gene

mRNA/cDNA for SAMD1 Gene

Unigene Clusters for SAMD1 Gene

Sterile alpha motif domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SAMD1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SAMD1 Gene

No ASD Table

Relevant External Links for SAMD1 Gene

GeneLoc Exon Structure for
SAMD1
ECgene alternative splicing isoforms for
SAMD1

Expression for SAMD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SAMD1 Gene

Protein differential expression in normal tissues from HIPED for SAMD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.5), Fetal testis (9.8), Fetal Brain (7.5), and Blymphocyte (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SAMD1 Gene



Protein tissue co-expression partners for SAMD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SAMD1 Gene:

SAMD1

SOURCE GeneReport for Unigene cluster for SAMD1 Gene:

Hs.140309

mRNA Expression by UniProt/SwissProt for SAMD1 Gene:

Q6SPF0-SAMD1_HUMAN
Tissue specificity: Expressed in atherosclerotic lesions, not in normal intima.

Evidence on tissue expression from TISSUES for SAMD1 Gene

  • Lung(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with SAMD1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SAMD1 Gene

Orthologs for SAMD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SAMD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SAMD1 34 33
  • 98.53 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SAMD1 33 34
  • 89.27 (n)
rat
(Rattus norvegicus)
Mammalia LOC102550189 33
  • 85.48 (n)
mouse
(Mus musculus)
Mammalia Samd1 33 16 34
  • 85.29 (n)
oppossum
(Monodelphis domestica)
Mammalia SAMD1 34
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SAMD1 34
  • 87 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii samd1a 34
  • 36 (a)
OneToMany
samd1b 34
  • 22 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG2662 34
  • 12 (a)
OneToMany
Species where no ortholog for SAMD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SAMD1 Gene

ENSEMBL:
Gene Tree for SAMD1 (if available)
TreeFam:
Gene Tree for SAMD1 (if available)

Paralogs for SAMD1 Gene

Paralogs for SAMD1 Gene

(4) SIMAP similar genes for SAMD1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SAMD1: view

Variants for SAMD1 Gene

Sequence variations from dbSNP and Humsavar for SAMD1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs8062 --

Structural Variations from Database of Genomic Variants (DGV) for SAMD1 Gene

Variant ID Type Subtype PubMed ID
dgv1716n106 CNV deletion 24896259
dgv49n68 CNV loss 17160897
dgv6274n54 CNV loss 21841781
dgv6275n54 CNV loss 21841781
dgv6276n54 CNV gain 21841781
dgv6277n54 CNV gain+loss 21841781
dgv6278n54 CNV loss 21841781
dgv6279n54 CNV loss 21841781
esv21807 CNV loss 19812545
esv2677290 CNV deletion 23128226
nsv1071913 CNV deletion 25765185
nsv578642 CNV gain 21841781
nsv578643 CNV loss 21841781
nsv578645 CNV loss 21841781
nsv578653 CNV gain 21841781
nsv578655 CNV gain 21841781
nsv578658 CNV loss 21841781
nsv828452 CNV loss 20364138
nsv828454 CNV gain 20364138
nsv828455 CNV gain 20364138
nsv833761 CNV loss 17160897
nsv953980 CNV deletion 24416366

Variation tolerance for SAMD1 Gene

Gene Damage Index Score: 1.99; 36.75% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SAMD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SAMD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SAMD1 Gene

Disorders for SAMD1 Gene

Relevant External Links for SAMD1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SAMD1

No disorders were found for SAMD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SAMD1 Gene

Publications for SAMD1 Gene

  1. Atherin: a newly identified, lesion-specific, LDL-binding protein in human atherosclerosis. (PMID: 16159594) Lees AM … Lees RS (Atherosclerosis 2005) 3 4 22 60
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  3. 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. (PMID: 27703004) Baas R … Marc Timmers HT (The Journal of biological chemistry 2016) 3 60
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 60
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 60

Products for SAMD1 Gene

Sources for SAMD1 Gene

Content
Loading form....