Our Favorite Gene: CLN1

A generic square image of CLN1 with rounded corners in a figure.
Title: Protein CLN1 of Saccharomyces cerevisiae

General Information

  • Standard Name: CLN1
  • Systematic Name: YMR199W
  • Name Description: cyclin CN1

Gene ID

  • SGD: S000004812
  • NCBI: SGD: S000004812 or Gene ID: 855239
  • Ensembl: SGD;Acc: S000004812, Gene ID: YMR199W
  • Uniprot: Taxonomic Identifier: P20437 [NCBI]

Plate control of protein CLN1 of Saccharomyces cerevisiae from an experiment analyzing protein localization and abundance changes during DNA replication stress (Tkach, J. M, et al., 2012).

Sequences

Gene Summary

CLN1 is a gene involved in protein coding found on the chromosome XIII (CLN1 | SGD, 2017). It encodes for a G1 cyclin which regulates the cell cycle meaning they activate CDKs at the correct times within the cell cycle. It can be found within the nucleus and the cytoplasm of the cell (CLN1 | SGD, 2017). To further characterize CLN1, the genomic sequence is NC_001145.3 and the name of the mRNA and protein Reference Sequences are NM_001182706.1 and NP_013926.1 respectively (CLN1 | SGD, 2017). Another primary way to identify the gene is through the locus name or tag: YMR199W. The processes CLN1 is involved in includes the cell cycle, cell division, and regulation of serine/threonine kinase activity. Lastly, to discuss the physical characteristics, the protein length was measured to be 546 a.a., the isoelectric point to be 5.62, and the molecular weight to be 62038.2 Da (CLN1 | SGD, 2017).

Written Responses

Function of CLN1: CLN1 Encodes for a G1 cyclin which regulates the cell cycle by activating CDKs at the correct times within the cell cycle thus promoting G1 phase to S phase.
Differences about the information provided in each of the parent databases: Most of the databases had similar if not overlapping information on CLN1. Most of the databases referenced SGD in particular which went much further in depth including experimental data, shared domains with other genes, and percentage of amino acid in the protein which was particularly interesting.
Differences in content, the information, or data itself: Most of the overall information was the same regarding data e.g. function, mRNA name, protein name, processes in which CLN1 is involved in and where it's found within the cell. The primary difference was the depth in which each of the sites went into regarding CLN1.
Differences in the presentation of the information: Most of the sites had easy navigation through the information on CLN1. The only site which was slightly more difficult to navigate was Ensembl because of the setup for the respective sections on the right side of the page. The other three databases had it in one single page and links to each section respectively.
Why we chose our gene: We chose our gene because we wanted to pick a gene associated with the cell cycle. Specifically, genes that have to do with cancer and mutations in genes that result in cancers e.g. tumor suppressors. Although there weren't tumor suppressor genes for yeast, possible issues with genes promoting the cell cycle was as close as we could go regarding yeast genes.

Ajax Requests


Ensembl

Loading…

NCBI

Loading…

Acknowledgements

The two of us met outside of class and worked on the project together. Eddie handled the website, while Antonio handled the content.

Made edits based off the feedback received from Dr. Dondi and Dr. Dalquist.

~Eddie Azinge and Antonio Porras

References

  1. Ensembl.org. (2017). Gene: CLN1 (YMR199W) - Supporting evidence - Saccharomyces cerevisiae - Ensembl genome browser 90. [online] Available at: https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Evidence?db=core;g=YMR199W;r=XIII:662644-664284;t=YMR199W [Accessed 26 Sep. 2017].
  2. Images.yeastrc.org. (2017). YRC Public Image Repository - Search Results. [online] Available at: http://images.yeastrc.org/imagerepo/searchImageRepo.do?verboseSearchResults=on&dataSource=0&includeFRET=1&channelModifier=3&channelCount=1&zsectionModifier=3&zsectionCount=1×eriesModifier=3×eriesCount=1&objective=0&binning=0&imageSize=0&proteinID=533021&proteinListing=CLN1&proteinID2=0&proteinListing2=&speciesID=0&strainName=&goAcc1=&goAccListing1=&goAcc2=&goAccListing2=&goAcc3=&goAccListing3=&goAcc4=&goAccListing4=&goAcc5=&goAccListing5= [Accessed 26 Sep. 2017].
  3. LMU BioDB 2017. (2017). Week 4. Retrieved September 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_4
  4. LMU BioDB 2017. (2017). Week 7. Retrieved October 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
  5. Ncbi.nlm.nih.gov. (2017). CLN1 cyclin CLN1 [Saccharomyces cerevisiae S288C] - Gene - NCBI. [online] Available at: https://www.ncbi.nlm.nih.gov/gene/855239 [Accessed 26 Sep. 2017].
  6. Uniprot.org. (2017). CLN1 - G1/S-specific cyclin CLN1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) - CLN1 gene & protein. [online] Available at: http://www.uniprot.org/uniprot/P20437#subcellular_location [Accessed 26 Sep. 2017].
  7. Yeastgenome.org. (2017). CLN1 | SGD. [online] Available at: https://www.yeastgenome.org/locus/S000004812 [Accessed 26 Sep. 2017].
  8. Tkach, J. M., Yimit, A., Lee, A. Y., Riffle, M., Costanzo, M., Jaschob, D., … Brown, G. W. (2012). Dissecting DNA damage response pathways by analyzing protein localization and abundance changes during DNA replication stress. Nature Cell Biology, 14(9), 966–976. http://doi.org/10.1038/ncb2549