Human Gene SLN (ENST00000305991.3_7) from GENCODE V47lift37
  Description: sarcolipin (from RefSeq NM_003063.3)
Gencode Transcript: ENST00000305991.3_7
Gencode Gene: ENSG00000170290.4_9
Transcript (Including UTRs)
   Position: hg19 chr11:107,578,104-107,582,782 Size: 4,679 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr11:107,578,561-107,578,656 Size: 96 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:107,578,104-107,582,782)mRNA (may differ from genome)Protein (31 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SARCO_HUMAN
DESCRIPTION: RecName: Full=Sarcolipin;
SUBUNIT: Associated with calcium ATPase SERCA1.
SUBCELLULAR LOCATION: Sarcoplasmic reticulum membrane; Single-pass membrane protein.
SIMILARITY: Belongs to the sarcolipin family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SLN
Diseases sorted by gene-association score: familial atrial fibrillation (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 727.69 RPKM in Muscle - Skeletal
Total median expression: 1100.37 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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.00169-0.314 Picture PostScript Text
3' UTR -111.20457-0.243 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008028 - Sarcolipin

Pfam Domains:
PF05366 - Sarcolipin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1JDM - NMR


ModBase Predicted Comparative 3D Structure on O00631
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004857 enzyme inhibitor activity
GO:0005515 protein binding
GO:0030234 enzyme regulator activity
GO:0051117 ATPase binding

Biological Process:
GO:0006816 calcium ion transport
GO:0043086 negative regulation of catalytic activity
GO:0043242 negative regulation of protein complex disassembly
GO:0051924 regulation of calcium ion transport
GO:0070296 sarcoplasmic reticulum calcium ion transport
GO:0090281 negative regulation of calcium ion import
GO:1901020 negative regulation of calcium ion transmembrane transporter activity
GO:1901077 regulation of relaxation of muscle
GO:1901877 negative regulation of calcium ion binding
GO:1901881 positive regulation of protein depolymerization
GO:1901894 regulation of calcium-transporting ATPase activity

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016529 sarcoplasmic reticulum
GO:0033017 sarcoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  BC094685 - Homo sapiens sarcolipin, mRNA (cDNA clone MGC:102826 IMAGE:6203008), complete cds.
BC005261 - Homo sapiens sarcolipin, mRNA (cDNA clone MGC:12301 IMAGE:3934241), complete cds.
U96094 - Human sarcolipin (SLN) mRNA, complete cds.
JD111605 - Sequence 92629 from Patent EP1572962.
JD520237 - Sequence 501261 from Patent EP1572962.
KJ901750 - Synthetic construct Homo sapiens clone ccsbBroadEn_11144 SLN gene, encodes complete protein.
JD424267 - Sequence 405291 from Patent EP1572962.
JD524178 - Sequence 505202 from Patent EP1572962.
BC104185 - Homo sapiens sarcolipin, mRNA (cDNA clone MGC:125853 IMAGE:40030832), complete cds.
BC113930 - Homo sapiens sarcolipin, mRNA (cDNA clone MGC:125855 IMAGE:40030834), complete cds.
BC113987 - Homo sapiens sarcolipin, mRNA (cDNA clone MGC:125854 IMAGE:40030833), complete cds.
BC104150 - Homo sapiens sarcolipin, mRNA (cDNA clone MGC:125721 IMAGE:40029313), complete cds.
JD200461 - Sequence 181485 from Patent EP1572962.
AK312097 - Homo sapiens cDNA, FLJ92379, Homo sapiens sarcolipin (SLN), mRNA.
KJ892159 - Synthetic construct Homo sapiens clone ccsbBroadEn_01553 SLN gene, encodes complete protein.
AB464701 - Synthetic construct DNA, clone: pF1KB8747, Homo sapiens SLN gene for sarcolipin, without stop codon, in Flexi system.
CR450290 - Homo sapiens full open reading frame cDNA clone RZPDo834B051D for gene SLN, sarcolipin; complete cds; without stopcodon.
JD401755 - Sequence 382779 from Patent EP1572962.
JD105807 - Sequence 86831 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000305991.1, ENST00000305991.2, NM_003063, O00631, Q6ICV3, SARCO_HUMAN, SLN , uc317nss.1, uc317nss.2
UCSC ID: ENST00000305991.3_7
RefSeq Accession: NM_003063.3
Protein: O00631 (aka SARCO_HUMAN)

-  Gene Model Information
  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.