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
Stanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
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
  Press "+" in the title bar above to open this section.

-  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
  Press "+" in the title bar above to open this section.

-  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
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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  
  Protein SequenceProtein Sequence  

-  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.