Human Gene SAMD1 (uc010xnl.2) Description and Page Index
  Description: Homo sapiens sterile alpha motif domain containing 1 (SAMD1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:14,199,229-14,201,232 Size: 2,004 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr19:14,199,229-14,201,232 Size: 2,004 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:14,199,229-14,201,232)mRNA (may differ from genome)Protein (538 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtPubMed
Stanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SAMD1_HUMAN
DESCRIPTION: RecName: Full=Atherin; AltName: Full=Sterile alpha motif domain-containing protein 1; Short=SAM domain-containing protein 1;
FUNCTION: May play a role in atherogenesis by immobilizing LDL in the atherial wall.
SUBCELLULAR LOCATION: Cytoplasm. Secreted.
TISSUE SPECIFICITY: Expressed in atherosclerotic lesions, not in normal intima.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.
CAUTION: Due to its high GC content it turned out to be difficult to sequence the 5' end of the gene encoding the N-terminal proline-rich region of the protein and to unambiguously determine which sequence is correct. We display the sequence described in PubMed:16159594. This sequence fits better with orthologous sequences but is not consistent with the human reference genome sequence.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.44 RPKM in Spleen
Total median expression: 802.23 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR021129 - SAM_type1

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)

SCOP Domains:
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on Q6SPF0
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005576 extracellular region
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC065477 - Homo sapiens sterile alpha motif domain containing 1, mRNA (cDNA clone IMAGE:3929733), partial cds.
BC030129 - Homo sapiens sterile alpha motif domain containing 1, mRNA (cDNA clone IMAGE:3943601), partial cds.
BC007384 - Homo sapiens sterile alpha motif domain containing 1, mRNA (cDNA clone IMAGE:3677194), partial cds.
BC080588 - Homo sapiens sterile alpha motif domain containing 1, mRNA (cDNA clone IMAGE:3542295), partial cds.
AY453840 - Homo sapiens atherin mRNA, complete cds.
JD390100 - Sequence 371124 from Patent EP1572962.
JD175407 - Sequence 156431 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_138352, NP_612361, Q6P0R3, Q6PIS7, Q6SPF0, Q96IM4, SAMD1_HUMAN
UCSC ID: uc010xnl.2
RefSeq Accession: NM_138352
Protein: Q6SPF0 (aka SAMD1_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138352.1
exon count: 6CDS single in 3' UTR: no RNA size: 1617
ORF size: 1299CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2166.00frame shift in genome: no % Coverage: 80.27
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.