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
  • Atherin 3 4
  • SAM Domain-Containing Protein 1 4
  • SAM Domain Containing 1 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. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is PHC2.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for SAMD1 Gene

Genomics for SAMD1 Gene

GeneHancer (GH) Regulatory Elements for SAMD1 Gene

Promoters and enhancers for SAMD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J014089 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 750.6 +0.1 135 3.8 ZNF24 ZBTB40 CTCF SMARCE1 POLR2A NR2F6 ZNF362 ELF1 L3MBTL2 TEAD4 SAMD1 ADGRL1 CACNA1A NANOS3 NACC1 SLC1A6 RF00017-2838 PRKACA
GH19J013951 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 4.6 +138.1 138141 2.6 SP1 ZBTB40 POLR2A CEBPZ CTBP1 ATF1 FOS CREB1 MIXL1 NFYC DCAF15 PODNL1 lnc-RFX1-2 CCDC130 DDX39A ADGRL1 ENSG00000267519 CACNA1A NANOS3 MRI1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SAMD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SAMD1 gene promoter:
  • E47
  • ITF-2
  • NF-kappaB
  • NF-kappaB1
  • p53
  • POU3F1
  • PPAR-gamma1
  • PPAR-gamma2
  • Tal-1beta

Genomic Locations for SAMD1 Gene

Genomic Locations for SAMD1 Gene
chr19:14,087,840-14,091,036
(GRCh38/hg38)
Size:
3,197 bases
Orientation:
Minus strand
chr19:14,198,652-14,201,848
(GRCh37/hg19)
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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SAMD1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SAMD1 Gene

GenScript: Design optimal peptide antigens:
  • Sterile alpha motif domain-containing protein 1 (SAMD1_HUMAN)
genes like me logo Genes that share domains with SAMD1: view

No data available for Graphical View of Domain Structure and 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.
genes like me logo Genes that share phenotypes with SAMD1: view

Animal Model Products

CRISPR Products

Clone Products

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 2
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

PathCards logo

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

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(167) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

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, 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

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 33 32
  • 98.53 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SAMD1 33 32
  • 89.27 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC102550189 32
  • 85.48 (n)
mouse
(Mus musculus)
Mammalia Samd1 17 33 32
  • 85.29 (n)
oppossum
(Monodelphis domestica)
Mammalia SAMD1 33
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SAMD1 33
  • 87 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii samd1a 33
  • 36 (a)
OneToMany
samd1b 33
  • 22 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG2662 33
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SAMD1: view image

Paralogs for SAMD1 Gene

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

  • SAMD1_HUMAN
  • E9PIW9_HUMAN
  • F8WDT5_HUMAN
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 Variation AA Info Type
rs1000525938 -- 14,091,050(-) C/A/G upstream_transcript_variant
rs1000575034 -- 14,088,357(-) T/C 3_prime_UTR_variant
rs1000807995 -- 14,089,633(-) A/C intron_variant
rs1001908965 -- 14,087,919(-) G/A 3_prime_UTR_variant
rs1002309675 -- 14,089,808(-) T/C coding_sequence_variant, missense_variant

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)

Additional Variant Information for SAMD1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for SAMD1 Gene

Additional Disease Information for 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 23 56
  2. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. (PMID: 29509190) Giurato G … Tarallo R (Scientific data 2018) 3 56
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56
  4. A High-Density Map for Navigating the Human Polycomb Complexome. (PMID: 27705803) Hauri S … Beisel C (Cell reports 2016) 3 56
  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. (PMID: 27703004) Baas R … Marc Timmers HT (The Journal of biological chemistry 2016) 3 56

Products for SAMD1 Gene

Sources for SAMD1 Gene