QLanners Week 4

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For this week's assignment, Emma Tyrnauer and I surfed the Saccharomyces Genome Database (SGD) after Thursday's class period. We picked the gene ADA2 as our favorite gene to focus on for the week.

To start this week's assignment, Emma and I decided to both individually do the initial research on the ADA2 gene using the four websites on the assignment page. I started my research by visiting the SGD website on 9/24. From here I obtained the following information:

  • Standard Name: ADA2
  • Systematic Name: YDR448W
  • Name Description: transcriptional ADAptor
  • Gene ID (from SGD): S000002856
  • Web address of gene to be used for hyperlink on webpage: https://www.yeastgenome.org/locus/S000002856
  • DNA Sequence:

1 ATGTCAAACA AGTTTCACTG TGACGTTTGT TCAGCTGATT GCACGAACAG AGTGAGGGTT
61 TCATGTGCTA TTTGTCCCGA ATACGACTTA TGCGTGCCCT GCTTTTCACA AGGCTCGTAT
121 ACAGGAAAGC ATCGCCCTTA CCATGATTAT AGGATAATAG AGACCAATTC ATACCCCATT
181 CTCTGTCCTG ATTGGGGTGC CGATGAAGAA TTGCAGTTGA TTAAAGGCGC ACAGACTTTA
241 GGGCTCGGTA ATTGGCAGGA TATTGCTGAC CATATAGGCA GCAGAGGCAA AGAAGAAGTT
301 AAGGAACATT ACCTAAAATA TTATCTGGAA AGCAAATACT ATCCAATACC TGATATTACC
361 CAAAATATAC ATGTCCCACA AGATGAATTT TTGGAACAGC GAAGGCATAG AATCGAGTCC
421 TTCCGGGAGA GGCCGCTAGA GCCTCCAAGA AAGCCCATGG CATCGGTTCC TAGCTGCCAT
481 GAAGTACAGG GGTTTATGCC GGGCAGATTA GAATTTGAAA CAGAATTCGA AAATGAAGCT
541 GAAGGTCCCG TAAAGGATAT GGTTTTTGAA CCTGATGACC AGCCCTTAGA CATTGAATTG
601 AAGTTTGCCA TCTTGGACAT TTACAATTCT AGATTGACAA CCAGAGCAGA AAAGAAAAGG
661 CTATTATTTG AAAACCATTT AATGGATTAC AGAAAGTTGC AAGCTATTGA CAAAAAGAGG
721 AGCAAAGAAG CCAAAGAATT GTATAACCGC ATAAAACCTT TTGCTCGTGT TATGACTGCA
781 CAGGATTTTG AGGAATTTAG CAAGGATATA TTAGAAGAAT TGCATTGCAG GGCAAGAATA
841 CAGCAATTAC AAGAATGGAG AAGCAATGGG TTAACCACGT TAGAAGCAGG TCTTAAGTAT
901 GAACGAGATA AGCAAGCTAG AATTAGCAGT TTCGAGAAAT TTGGCGCTTC TACGGCGGCG
961 TCACTCAGTG AGGGCAATAG CCGTTATAGG TCGAATTCTG CACATAGGTC GAACGCAGAA
1021 TACAGCCAAA ACTACAGCGA AAATGGCGGT AGAAAGAAAA ATATGACCAT TAGCGATATA
1081 CAGCATGCAC CTGACTATGC ACTGTTGTCC AACGACGAGC AGCAACTTTG TATTCAACTG
1141 AAAATTTTAC CTAAACCGTA TCTCGTTCTA AAAGAGGTAA TGTTCAGAGA ACTGTTGAAG
1201 ACTGGGGGTA ATCTAAGCAA AAGCGCATGT AGGGAACTAC TTAATATAGA CCCCATAAAA
1261 GCGAATAGAA TATACGATTT TTTCCAGAGC CAGAATTGGA TGTAA

  • Protein Sequence:

1 MSNKFHCDVC SADCTNRVRV SCAICPEYDL CVPCFSQGSY TGKHRPYHDY RIIETNSYPI
61 LCPDWGADEE LQLIKGAQTL GLGNWQDIAD HIGSRGKEEV KEHYLKYYLE SKYYPIPDIT
121 QNIHVPQDEF LEQRRHRIES FRERPLEPPR KPMASVPSCH EVQGFMPGRL EFETEFENEA
181 EGPVKDMVFE PDDQPLDIEL KFAILDIYNS RLTTRAEKKR LLFENHLMDY RKLQAIDKKR
241 SKEAKELYNR IKPFARVMTA QDFEEFSKDI LEELHCRARI QQLQEWRSNG LTTLEAGLKY
301 ERDKQARISS FEKFGASTAA SLSEGNSRYR SNSAHRSNAE YSQNYSENGG RKKNMTISDI
361 QHAPDYALLS NDEQQLCIQL KILPKPYLVL KEVMFRELLK TGGNLSKSAC RELLNIDPIK
421 ANRIYDFFQS QNWM*

  • Function of your gene:
    • Binding to chromatin
    • Catalysis the reaction of acetyl-CoA with histone to make CoA and acetyl-histone
    • Phosphatidylserine binding
    • transcription coactivator activity to increase the frequency, rate, or duration of transcription

After obtaining this general information on the gene, Emma and I met the following day (9/25) to work together on the website. Using the notes we had both previously taken we were easily able to complete the majority of the assignment, as the content had already been obtained. We worked together, and used Bootstraps code, to put this content into a webpage format. Working on the Lanners-Tyrnauer.html file (which we had previously downloaded in class) we edited the HTML template.

The bulk of the information was put into simple paragraph form, with headers being used to denote each section. However, we did decide to use a few unique features to display our data. We used a table to format the different ID#s of the gene from each of the four databases. Inside of this table we included links to both the general database website and the particular page of the ADA2 gene within that database.

Along with this table, we thought a carousel would be very effective to show the pros/cons/unique features of each database. This feature allows the webpage viewer to toggle between different slides to read on each database individually. Using Bootstraps code for carousels we were easily able to format this.

Finally, we worked together as a group to answer the question of why we chose ADA2 as our gene and also completing the references and acknowledgements for the page. Overall, we were able to complete the webpage in a very timely manner due to the fact that we did it together in person and had each done research on our gene prior to meeting.

After meeting with Emma, I looked through the webpage for any formatting errors and/or typos. After fixing all the errors that I had found, I uploaded the file. The final zip file for this assignment is below:
File:Lanners-Tyrnauer 2.zip


Acknowledgements

  • I met with my homework partner Emma Tyrnauer outside of class to work together on the webpage using notes we had taken prior.
  • Dr. Dondi for teaching us how to navigate HTML and use Bootstrap
  • Dr. Dahlquist for the lesson on how to analyze the quality of a database

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Qlanners (talk) 15:32, 25 September 2017 (PDT)


References

Bootstrap. (2017). Documentation. Retrieved September 25, 2017, from https://getbootstrap.com/docs/4.0/getting-started/introduction/
Ensembl. (2017). "Gene: ADA2". Retrieved September 24, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Summary?db=core;g=YDR448W;r=IV:1356065-1357369;t=YDR448W
LMU BioDB 2017. (2017). Week 4. Retrieved September 25, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_4
NCBI. (2017). "ADA2 chromatin-binding transcription regulator". Retrieved September 24, 2017, from https://www.ncbi.nlm.nih.gov/gene/852059
Saccharomyces Genome Database. (2017). "ADA2/YDR448W Overview". Retrieved September 24, 2017, from https://www.yeastgenome.org/locus/S000002856
UniProt. (2017). "Q02336 (ADA2_Yeast)". Retrieved September 24, 2017, from http://www.uniprot.org/uniprot/Q02336
WikiMedia Commons. (2015). "File:Type ii nuclear receptor action.png". Retrieved September 25, 2017, from https://commons.wikimedia.org/wiki/File:Type_ii_nuclear_receptor_action.png

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