Human Gene CSN1S1 (ENST00000246891.9_12) from GENCODE V47lift37
  Description: casein alpha s1, transcript variant 1 (from RefSeq NM_001890.2)
Gencode Transcript: ENST00000246891.9_12
Gencode Gene: ENSG00000126545.14_17
Transcript (Including UTRs)
   Position: hg19 chr4:70,796,786-70,812,292 Size: 15,507 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr4:70,798,274-70,811,914 Size: 13,641 Coding Exon Count: 15 

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 (chr4:70,796,786-70,812,292)mRNA (may differ from genome)Protein (185 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CASA1_HUMAN
DESCRIPTION: RecName: Full=Alpha-S1-casein; Contains: RecName: Full=Casoxin-D; Flags: Precursor;
FUNCTION: Important role in the capacity of milk to transport calcium phosphate.
FUNCTION: Casoxin D acts as opioid antagonist and has vasorelaxing activity mediated by bradykinin B1 receptors.
SUBUNIT: Heteromultimers of alpha-s1 casein and kappa-casein; disulfide-linked.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Mammary gland specific. Secreted in milk.
PTM: Not glycosylated.
MISCELLANEOUS: In milk, the alpha s1- and beta-caseins precipitate in presence of calcium (so-called calcium-sensitive caseins). Kappa-casein prevents the precipitation of the other caseins by calcium through the formation of large stable colloidal particles termed micelles.
SIMILARITY: Belongs to the alpha-casein family.
WEB RESOURCE: Name=Protein Spotlight; Note=Of buttons, digestion and glue - Issue 16 of November 2001; URL="http://web.expasy.org/spotlight/back_issues/sptlt016.shtml";

-  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: CSN1S1
Diseases sorted by gene-association score: milk allergy (12), goat milk allergy (8), food allergy (6), allergic hypersensitivity disease (3), atrophy of testis (3), autoimmune enteropathy (3), autoinflammation with infantile enterocolitis (2), mycetoma (2), pelvic varices (2), aplasia of lacrimal and salivary glands (1)

-  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: 2.23 RPKM in Adipose - Subcutaneous
Total median expression: 4.45 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 -7.3062-0.118 Picture PostScript Text
3' UTR -82.60378-0.219 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
IPR026999 - Alpha-s1_casein
IPR001588 - Casein

ModBase Predicted Comparative 3D Structure on P47710
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0055085 transmembrane transport

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  JD246084 - Sequence 227108 from Patent EP1572962.
X78416 - H.sapiens alpha-s1-casein mRNA.
BC128227 - Homo sapiens casein alpha s1, mRNA (cDNA clone MGC:149367 IMAGE:40114618), complete cds.
BC128228 - Homo sapiens casein alpha s1, mRNA (cDNA clone MGC:149368 IMAGE:40114622), complete cds.
U23157 - Human pro-alpha-S1-casein mRNA, complete cds.
JD320344 - Sequence 301368 from Patent EP1572962.
KJ896659 - Synthetic construct Homo sapiens clone ccsbBroadEn_06053 CSN1S1 gene, encodes complete protein.
AB528963 - Synthetic construct DNA, clone: pF1KB6816, Homo sapiens CSN1S1 gene for casein alpha s1, without stop codon, in Flexi system.
DQ064604 - Homo sapiens casein mRNA, complete cds.
X98084 - H.sapiens mRNA for alpha S1-casein.
JD494707 - Sequence 475731 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A1A510, A1A511, CASA, CASA1_HUMAN, CSN1, E9PB60, ENST00000246891.1, ENST00000246891.2, ENST00000246891.3, ENST00000246891.4, ENST00000246891.5, ENST00000246891.6, ENST00000246891.7, ENST00000246891.8, NM_001890, P47710, Q4PNR5, uc317eum.1, uc317eum.2
UCSC ID: ENST00000246891.9_12
RefSeq Accession: NM_001890.2
Protein: P47710 (aka CASA1_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.