CMR2/YOR093C Week 3

Individual Journal Assignment

• Store this journal entry as "gene name Week 3" (i.e., this is the text to place between the square brackets when you link to this page). Each partner will contribute to one journal page for this week.
• Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.) Each partner would invoke their template on the shared page.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Don't forget to add the "Journal Entry" category to the end of your wiki page.

Paper and Pencil Assignment

You will turn in individually the completed paper and pencil assignment that was handed out in class on Thursday, 9/12/19. The paper copy is due at the beginning of class on Thursday, 9/19/19.

“My Favorite Gene”

With your homework partner, you will create a wiki page (one page shared by both partners) that displays the relevant information for a “favorite gene.” (OK, so maybe you don’t really have a favorite gene—but it makes for a fun assignment title)

For this exercise (and the rest of the semester), we will focus on budding yeast (a.k.a. Baker's yeast, Brewer's yeast, Saccharomyces cerevisiae) as a model organism. A model organism is used for research because it has some property that makes it easy to study the phenomenon of interest. Budding yeast is a simple, single-celled eukaryote that shares fundamental properties with human cells, yet is much easier to study. A lot of foundational work in understanding cancer, for example, was performed in yeast.

For the Week 3 exercise, you will select your favorite yeast gene to highlight.

1. To choose your gene, visit the Saccharomyces Genome Database (SGD), a model organism database that aims to be a one-stop shop for yeast data.
   • You can search for a gene or protein in the search field or browse the resources at the site through the various tabs. If you do not already have a gene in mind that you want to find, the curators at SGD maintain a blog to highlight interesting research. Browse through the Research Spotlights or Yeast and Human Disease categories for inspiration.
   • You may not use the same gene as another group. Gene choices are first-come, first-served. To claim your gene, edit this page, listing the gene you have chosen next to the names of you and your homework partners.
2. Once you have identified your gene, you will look it up in four different databases and create a summary of what you have learned about your gene on you and our partner's wiki page. The four databases are:
   • SGD itself
   • NCBI Gene Database
   • Ensembl
   • UniProt
   • The summary should be one paragraph about the function of your gene based on what you have read in each of the four databases. This is one paragraph that synthesizes information, not one paragraph per database.
3. Provide the following additional information about your gene on your wiki page:
   1. What is the standard name, systematic name, and name description for your gene (from SGD)?

• A. Standard Name CMR2, Systematic Name: YOR093C, Name Description: Changed Mutation Rate

1. 1. What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?

A. SGD:S000005619, NCBI: 854260, Ensemble: R64-1-1:BK006948.2, UniPort: 559292

1. 1. • Provide hyperlinks to the specific pages for your gene in each of the above databases.

• SGD
• UniPort
• Ensembl
• NCBI

1. 1. What is the DNA sequence of your gene?

1 ATGGATTTTT CTATTCCTCC TACCTTACCT CTAGATCTGC AAAGTCGGTT AAATGAGTTA 
 61 ATTCAAGACT ATAAGGATGA AAATCTAACA AGAAAGGGTT ATGAGACCAA AAGAAAACAA 
121 TTGCTAGACA AATTTGAAAT CTCCCAAATG AGGCCTTATA CCCCGCTTCG ATCTCCCAAT 
181 TCGAGAAAGT CGAAACATTT GCACAGAAGA AATACAAGTC TTGCATCATC CATTACGTCG 
241 TTACCTAATT CAATTGACAG ACGTCATTCT ATCTATCGTG TCACAACTAT AAACTCGACT 
301 TCTGCGAACA ATACTCCCAG AAGGCGGAGC AAGAGATATA CAGCTTCTTT GCAATCGTCA 
361 TTGCCAGGTT CCAGTGATGA AAACGGTTCA GTGAAGGATG CCGTTTATAA TCCTATGATA 
421 CCATTACTAC CAAGACACAC TGGAGCCGAA AATACTAGCA GTGGAGACTC AGCAATGACG 
481 GATTCTTTAC CGCTAATTTT ACGGGGACGC TTTGAACATT ATGATGGTCA AACAGCGATG 
541 ATCAGCATAA ATTCTAAAGG CAAAGAAACG TTCATCACAT GGGATAAACT TTATTTGAAA 
601 GCGGAGAGGG TAGCACATGA ATTGAATAAG AGTCACCTTT ACAAAATGGA TAAGATTTTA 
661 CTATGGTACA ATAAAAATGA TGTCATCGAA TTTACTATTG CATTATTAGG CTGTTTCATA 
721 TCCGGCATGG CAGCTGTACC AGTCTCATTC GAAACGTATT CTCTGCGTGA GATCCTTGAG 
781 ATAATTAAAG TAACAAATTC GAAATTTGTT CTGATTTCTA ACGCATGTCA TAGACAATTA 
841 GATAACTTGT ATTCGTCATC AAATCATTCA AAAGTTAAAC TGGTTAAGAA CGATGTTTTC 
901 CAGCAAATCA AATTTGTCAA GACTGATGAC TTAGGGACGT ACACAAAGGC AAAAAAAACT 
961 TCGCCTACCT TTGATATACC GAATATTTCA TATATAGAGT TTACTAGAAC ACCGCTAGGT 

1021 CGTCTTTCTG GCGTCGTCAT GAAGCATAAC ATCTTAATAA ACCAATTTGA AACGATGACA 1081 AAAATTCTAA ACTCACGATC AATGCCTCAC TGGAAACAAA AATCACAAAG CATCAGGAAG 1141 CCATTTCACA AAAAAATTAT GGCAACCAAC TCAAGGTTTG TTATCTTGAA TAGTCTGGAC 1201 CCTACTAGAT CTACTGGTTT GATAATGGGT GTGCTTTTCA ATCTTTTTAC TGGTAATCTT 1261 ATGATATCTA TCGATAGTAG TATATTACAA CGACCTGGGG GCTATGAAAA TATCATTGAT 1321 AAATTTAGAG CCGACATTTT ACTGAATGAT CAGCTACAAT TGAAGCAGGT AGTTATTAAT 1381 TATTTGGAAA ATCCCGAATC AGCTTTTTCC AAGAAGCACA AAATAGATTT CAGTTGCATC 1441 AAGTCATGTT TAACCTCATG TACCACTATA GATACCGATG TAAGCGAGAT GGTTGTTCAT 1501 AAATGGCTGA AAAATTTAGG ATGTATTGAT GCACCATTTT GTTATTCTCC CATGTTAACG 1561 TTATTGGACT TTGGTGGTAT CTTTATATCT ATAAGAGATC AATTAGGAAA CCTAGAGAAC 1621 TTTCCAATAC ATAATTCAAA ACTAAGGCTT CAAAATGAAT TGTTTATAAA CCGCGAGAAA 1681 TTGAAGCTTA ATGAGGTTGA ATGTAGCATA ACTGCTATGA TTAATTCATC AAGCTCCTTC 1741 AAAGATTATC TTAAATTAGA AACATTTGGC TTCCCAATTC CTGATATCAC TTTATGTGTG 1801 GTTAATCCAG ATACGAATAC GTTGGTGCAA GACCTCACTG TTGGAGAAAT ATGGATCTCT 1861 TCTAACCACA TCACCGACGA ATTTTACCAG ATGGATAAAG TGAACGAATT TGTGTTCAAA 1921 GCAAAACTAA ATTACTCCGA AATGTTTTCT TGGGCAAAGT ATGAAATGCC TACTAACGAA 1981 AAATCGCAAG CAGTTACTGA ACAATTGGAT ACCATTCTGA ATATTTGTCC TGCAAATACC 2041 TACTTTATGA GAACCAAGCT TATGGGGTTT GTTCATAACG GAAAGATATA CGTGCTTTCA 2101 CTCATAGAAG ATATGTTTTT ACAGAATAGA TTAATCAGAT TACCTAACTG GGCTCACACA 2161 TCAAACCTTC TTTATGCCAA AAAAGGGAAT CAATCTGCTC AACCTAAAGG TAACACTGGA 2221 GCAGAAAGCA CTAAGGCTAT TGATATTTCG AGTTTAAGTG GCGAAACATC TTCGGGATAC 2281 AAAAGAGTTG TTGAATCCCA CTATCTACAA CAGATTACTG AAACAGTTGT GAGGACAGTA 2341 AATACAGTTT TTGAGGTTGC TGCATTTGAA TTACAACACC ATAAAGAAGA GCACTTTTTA 2401 GTTATGGTGG TAGAAAGCTC CCTAGCAAAA ACCGAAGAAG AGAGTAAAAA TGGCGAAACA 2461 ACAGATACTA CCTTAATGAA ATTTGCAGAA ACACAGAGGA ACAAATTAGA AACGAAAATG 2521 AATGATTTAA CTGACCAAAT TTTTAGAATT CTTTGGATTT TTCATAAAAT CCAACCAATG 2581 TGCATTTTAG TTGTGCCGAG AGATACTTTA CCTAGGAGAT ATTGTTCTCT GGAATTGGCC 2641 AATAGCACGG TAGAGAAGAA GTTTTTAAAC AATGATCTCA GTGCACAGTT TGTAAAGTTT 2701 CAATTCGATA ATGTCATATT GGATTTTTTG CCCCATTCAG CGTACTATAA TGAGAGTATA 2761 TTATCCGAGC ATTTATCAAA ATTGAGAAAG ATGGCTTTAC AAGAAGAATA CGCTATGATC 2821 GAACCAGCAT ATCGTAATGG CGGTCCCGTT AAACCAAAAC TTGCCCTACA ATGCAGTGGT 2881 GTTGATTACA GAGATGAGTC TGTTGACACT CGAAGCCATA CAAAACTCAC AGACTTCAAA 2941 TCGATTTTAG AGATTCTGGA ATGGAGAATT TCTAATTATG GGAACGAAAC GGCGTTCAGT 3001 GATGGTACAA ACACAAACCT AGTCAACTCT TCAGCTAGTA ACGATAATAA CGTTCACAAA 3061 AAGGTATCAT GGGCAAGTTT TGGTAAAATT GTCGCAGGCT TTTTGAAAAA AATCGTAGGT 3121 TCTAAAATTC CATTGAAGCA TGGTGACCCT ATTATTATTA TGTGTGAAAA TTCGGTTGAA 3181 TACGTAGCGA TGATCATGGC CTGCCTGTAC TGTAACTTAT TGGTAATTCC CCTACCAAGC 3241 GTTAAGGAGT CTGTCATAGA AGAGGACCTA AAAGGCTTGG TTAATATTAT TCAAAGTTAC 3301 AAAGTGAAAA GAGTATTTGT TGATGCTAAA TTGCACTCAT TGTTGAATGA TAATAATGTC 3361 GTAAACAAAT GTTTTAAGAA ATACAAAAGT TTGATACCCA AGATTACAGT TTTCTCAAAA 3421 GTCAAGACAA AGAATGCGTT AACAGTATCT ATGTTTAAGA ATGTGTTAAA GCAGAAATTT 3481 GGGGCCAAAC CAGGTACTAG GATTGGTATG ACACCGTGTG TTGTATGGGT AAATACAGAG 3541 TATGATGTAA CATCTAATAT TCACGTAACA ATGACACATT CGTCTTTACT GAATGCAAGC 3601 AAAATAGTCA AAGAAACTTT GCAGTTAAGA AATAATAGTC CACTTTTCTC TATATGTTCT 3661 CATACATCTG GATTGGGCTT TATGTTCAGC TGTTTGTTAG GAATTTATAC GGGTGCTTCA 3721 ACTTGCTTAT TCAGCCTTAC TGATGTTCTT ACTGACCCTA AGGAGTTTTT AATTGGCCTT 3781 CAAAATTTAA ACGTAAAAGA TTTATATTTG AAGCTTGAAA CGTTATATGC TTTACTGGAT 3841 AGAGCCTCTA GTTTGATTGA GGGATTCAAA AATAAGAAGG AGAATATAAA CTCTGCCAAA 3901 AACAATACAT CTGGCTCGCT TAGAGAAGAT GTTTTCAAGG GTGTTCGAAA TATCATGATA 3961 CCTTTTCCTA ATAGACCAAG GATTTATACA ATTGAAAATA TTTTAAAACG GTACTCAACC 4021 ATATCCCTAT CATGTACACA AATAAGTTAT GTCTATCAAC ATCACTTCAA TCCGCTTATA 4081 TCATTAAGGT CGTATCTGGA TATTCCTCCG GTTGACCTAT ATTTAGACCC ATTTTCACTG 4141 AGGGAAGGTA TAATTAGAGA AGTCAACCCC AATGATGTAA GTGCTGGAAA CTATATCAAG 4201 ATTCAAGATT CTGGTGTTGT TCCTGTATGT ACTGACGTTT CAGTAGTTAA TCCAGAGACA 4261 CTCCTACCAT GTGTTGATGG AGAATTCGGT GAGATTTGGT GCTGTTCGGA AGCTAATGCA 4321 TTCGACTACT TTGTGTGTAA CAGTTCAAAA AACAAGTTGT ACAAAGATCC CTTTATCACA 4381 GAACAATTCA AAAGTAAGAT GAAGAGCGAA GTGAATAACA CTTTAAGCTA TTTGAGAACT 4441 GGTGATCTGG GCTTTATCAA AAACGTAAGT TGCACGAATT CACAGGGAGA GGTCGTCAAT 4501 TTGAACTTGT TGTTTGTTTT GGGAAGTATT CATGAATCCA TTGAAATTCT AGGATTGACA 4561 CATTTTGTTA GTGATTTGGA GAGAACCGTT AAAGATGTTC ACAGTGACAT TGGTAGTTGT 4621 TTGATTGCCA AAGCAGGTGG ATTATTAGTG TGCTTAATTA GGTGTAAGGA ACGACATAAT 4681 CCCATCTTGG GTAATCTAAC GACTTTAATT GTTTCAGAGT TGTTAAATAA GCATGGTGTC 4741 ATTTTAGATT TATGCACATT TGTGAGAACT AAAGGTATAA GCCCAAAAAA TTCTAGTATG 4801 ATAATGGAAG TTTGGGCGAA AAATAGAGCA TCGATAATGC AAGCCTGGTT TGATCAGAAA 4861 ATTCAAATAG AAGCACAATT TGGCATAAAC TATGGTGAAA ATATTTCCAT TTATTTATTA 4921 TCAGATTATG AAAAGGACAA TATTTAA

1. 1. What is the protein sequence corresponding to your gene?

 1 MDFSIPPTLP LDLQSRLNEL IQDYKDENLT RKGYETKRKQ LLDKFEISQM RPYTPLRSPN 

 61 SRKSKHLHRR NTSLASSITS LPNSIDRRHS IYRVTTINST SANNTPRRRS KRYTASLQSS 

121 LPGSSDENGS VKDAVYNPMI PLLPRHTGAE NTSSGDSAMT DSLPLILRGR FEHYDGQTAM 

181 ISINSKGKET FITWDKLYLK AERVAHELNK SHLYKMDKIL LWYNKNDVIE FTIALLGCFI 

241 SGMAAVPVSF ETYSLREILE IIKVTNSKFV LISNACHRQL DNLYSSSNHS KVKLVKNDVF 

301 QQIKFVKTDD LGTYTKAKKT SPTFDIPNIS YIEFTRTPLG RLSGVVMKHN ILINQFETMT 

361 KILNSRSMPH WKQKSQSIRK PFHKKIMATN SRFVILNSLD PTRSTGLIMG VLFNLFTGNL 

421 MISIDSSILQ RPGGYENIID KFRADILLND QLQLKQVVIN YLENPESAFS KKHKIDFSCI 

481 KSCLTSCTTI DTDVSEMVVH KWLKNLGCID APFCYSPMLT LLDFGGIFIS IRDQLGNLEN 

541 FPIHNSKLRL QNELFINREK LKLNEVECSI TAMINSSSSF KDYLKLETFG FPIPDITLCV 

601 VNPDTNTLVQ DLTVGEIWIS SNHITDEFYQ MDKVNEFVFK AKLNYSEMFS WAKYEMPTNE 

661 KSQAVTEQLD TILNICPANT YFMRTKLMGF VHNGKIYVLS LIEDMFLQNR LIRLPNWAHT 

721 SNLLYAKKGN QSAQPKGNTG AESTKAIDIS SLSGETSSGY KRVVESHYLQ QITETVVRTV 

781 NTVFEVAAFE LQHHKEEHFL VMVVESSLAK TEEESKNGET TDTTLMKFAE TQRNKLETKM 

841 NDLTDQIFRI LWIFHKIQPM CILVVPRDTL PRRYCSLELA NSTVEKKFLN NDLSAQFVKF 

901 QFDNVILDFL PHSAYYNESI LSEHLSKLRK MALQEEYAMI EPAYRNGGPV KPKLALQCSG 

961 VDYRDESVDT RSHTKLTDFK SILEILEWRI SNYGNETAFS DGTNTNLVNS SASNDNNVHK 

1021 KVSWASFGKI VAGFLKKIVG SKIPLKHGDP IIIMCENSVE YVAMIMACLY CNLLVIPLPS
1081 VKESVIEEDL KGLVNIIQSY KVKRVFVDAK LHSLLNDNNV VNKCFKKYKS LIPKITVFSK
1141 VKTKNALTVS MFKNVLKQKF GAKPGTRIGM TPCVVWVNTE YDVTSNIHVT MTHSSLLNAS
1201 KIVKETLQLR NNSPLFSICS HTSGLGFMFS CLLGIYTGAS TCLFSLTDVL TDPKEFLIGL
1261 QNLNVKDLYL KLETLYALLD RASSLIEGFK NKKENINSAK NNTSGSLRED VFKGVRNIMI
1321 PFPNRPRIYT IENILKRYST ISLSCTQISY VYQHHFNPLI SLRSYLDIPP VDLYLDPFSL
1381 REGIIREVNP NDVSAGNYIK IQDSGVVPVC TDVSVVNPET LLPCVDGEFG EIWCCSEANA
1441 FDYFVCNSSK NKLYKDPFIT EQFKSKMKSE VNNTLSYLRT GDLGFIKNVS CTNSQGEVVN
1501 LNLLFVLGSI HESIEILGLT HFVSDLERTV KDVHSDIGSC LIAKAGGLLV CLIRCKERHN
1561 PILGNLTTLI VSELLNKHGV ILDLCTFVRT KGISPKNSSM IMEVWAKNRA SIMQAWFDQK
1621 IQIEAQFGIN YGENISIYLL SDYEKDNI*

1. 1. • Go to the ExPASy tool and translate the DNA sequence of your gene. Which reading frame encodes the protein sequence? Take a screenshot of your results, display it on your wiki page, and state which frame it is.
   2. What is the function of your gene?
   3. What was different about the information provided about your gene in each of the parent databases?
      • Were there differences in content, the information or data itself?
      • Were there differences in presentation of the information?
   4. Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
   5. Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
      • Please make the image something scientific (not like the random images seen on the SGD blog posts).
      • If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too.
   6. Include Acknowledgments and References sections on your wiki page. Both partners should sign the Academic Honesty statement with their wiki signatures.
      • You need to cite the specific database page from which you derived your information for each of the questions.
      • When answering the free-form questions, be sure to paraphrase.

Were there differences in presentation of the information? Why did you choose your particular gene? i.e., why is it interesting to you and your partner? Include an image related to your gene (be careful that you do not violate any copyright restrictions!) Please make the image something scientific (not like the random images seen on the SGD blog posts). If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too. Include Acknowledgments and References sections on your wiki page. Both partners should sign the Academic Honesty statement with their wiki signatures. You need to cite the specific database page from which you derived your information for each of the questions. When answering the free-form questions, be sure to paraphrase.