MSymond1 KMill104 Week 3 - Revision history

Kmill104: /* Acknowledgements */ formatting edit

2024-02-01T00:58:18Z

‎Acknowledgements: formatting edit

Kmill104: expanding on 6 and adding another reference

2024-02-01T00:57:35Z

expanding on 6 and adding another reference

Msymond1: /* Acknowledgements */ added Jmol4

2024-01-31T23:20:41Z

‎Acknowledgements: added Jmol4

Msymond1: /* Additional Information */ added ensemble

2024-01-31T23:14:24Z

‎Additional Information: added ensemble

Msymond1: added more to acknowledgements

2024-01-31T21:51:17Z

added more to acknowledgements

Msymond1: added signature

2024-01-31T21:47:40Z

added signature

Msymond1: added back the protein sequence

2024-01-31T21:43:14Z

added back the protein sequence

Msymond1: added the reading frame

2024-01-31T21:38:23Z

added the reading frame

Msymond1: /* Additional Information */ shrank frame

2024-01-31T21:26:30Z

‎Additional Information: shrank frame

Msymond1: added photo of protein

2024-01-31T21:24:48Z

added photo of protein

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 # Picture of structure[[image:MSN1.png|200px]]
 ===Acknowledgements===
-*I worked with my homework partner Dean Symonds [[MSymond1]] to complete this assignment. We worked together in class and texted once to ask a question. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
+*I worked with my homework partner Dean Symonds [[MSymond1]] to complete this assignment. We worked together in class and texted once to ask a question. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 12:51, 31 January 2024 (PST)
 *I worked with my homework partner, Katie Miller, we texted briefly. We also worked together in class to choose the gene. The picture of the structure was obtained using Jmol4 [https://proteopedia.org/wiki/fgij/fg.htm?mol=/wiki/fgijDATA/b6383740d762c5f8f62ee6d52dcd2efc/data.pdb link] Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:47, 31 January 2024 (PST)

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 #Protein Sequence - MASNQHIGASNLNENEAILTNRVAELERRMSMFEGIFHALSNRLDLHFKKYDVVVNSQQQQINELTAFLSTLLNDQQRHAEILSEKLSGTLHGVSATSISLSQTLDPQGFTDGTTAPGAPRYTSVPMNNDQTAHPQNEGAVSNETLFEDILNGNSQENDKSQQQTNSSNSISQENNSTNPSVDTRFNKPQNYNSNLVPSLEEYSANPPNNDGGQSQGLYISSNSSQSRQSPNLQKVSPNHENAVESNAQESVPTFEEEQYETKTGLKRKRIVCTRPFEFIKSPHSVMEVWKEYTEGVNGQPSIRKMEALYQTAWRRDPAVNKRYSRRKVLWKAIQTGLNRGYSLNYVVEILENSRYVNDKQKVKQPIGWLCHSSHIPETLK The sequence is in reading frame 1 [[image:Proteinframe.png|200px|]]
 #The primary function of our gene is to code for a protein that positively regulates transcription. The protein specifically acts in response to environmental stress so that transcription still occurs.
-#Each database had a section at the top with general information regarding the gene, like its name, organism, and other common descriptors. The UniProt database had a more detailed summary of the protein our gene codes for. UniProt referenced other genes and proteins that our gene/protein may interact with in order to positively regulate transcription. The description also mentioned that a specifically iron deficient environment will have enhanced growth when MSN1 is present. Both SGD and NCBI had less detailed summaries of the gene where they just listed its function as coding for a protein that positively regulates transcription. After going further down the page, each database had more detailed sections regarding specific functions, processes, and components. SGD had a large summary concerning regulation of the gene, while NCBI had a table summarizing the interactions between MSN1 and other genes. NCBI also provided related articles in PubMed. UniProt was the only database to provide an image of the protein’s structure. The presentation of information was different in the way that specific sections were organized and where they were placed on the page. Both SGD and NCBI has the gene sequence near the top of the page, while UniProt had it further down. SGD had a bar graph to illustrate expression of the gene, which was unique to its database. NCBI had little images except for the gene sequence, while UniProt had images of both the nucleus and the protein’s structure.
+#Each database had a section at the top with general information regarding the gene, like its name, organism, and other common descriptors. The UniProt and Ensembl databases had a more detailed summary of the protein our gene codes for. UniProt referenced other genes and proteins that our gene/protein may interact with in order to positively regulate transcription. The description also mentioned that a specifically iron deficient environment will have enhanced growth when MSN1 is present. The Ensembl database listed some processes of the protein in its description, like iron uptake and chromium accumulation. Both SGD and NCBI had less detailed summaries of the gene where they just listed its function as coding for a protein that positively regulates transcription. After going further down the page, each database had more detailed sections regarding specific functions, processes, and components. SGD had a large summary concerning regulation of the gene, while NCBI had a table summarizing the interactions between MSN1 and other genes. NCBI also provided related articles in PubMed. UniProt was the only database to provide an image of the protein’s structure. The presentation of information was different in the way that specific sections were organized and where they were placed on the page. Both SGD and NCBI has the gene sequence near the top of the page, while UniProt and Ensembl had it further down. SGD had a bar graph to illustrate expression of the gene, which was unique to its database. Ensembl was the only database where you had to click on links in the sidebar to get to certain sections. Ensembl also had a table dedicated to listing known variants of the gene and their alleles. NCBI had little images except for the gene sequence, while UniProt had images of both the nucleus and the protein’s structure.
 #We chose this gene because we were originally interested in proteins that could bind to DNA for some specific purpose. We thought it particularly interesting that this DNA-binding protein acted as a transcriptional regulator for cells that were in environmental stress. We wanted to learn more about how a protein can combat stressors so that transcription isn’t inhibited.
 # Picture of structure[[image:MSN1.png|200px]]
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 *National Center for Biotechnology Genome Database. (2024). MSN1 Msn1p [Saccharomyces cerevisiae S288C]. Retrieved January 31, 2024, from https://www.ncbi.nlm.nih.gov/gene/854033
 *UniProt. (2024). P22148 · MSN1_YEAST. Retrieved January 31, 2024, from https://www.uniprot.org/uniprotkb/P22148/entry

@@ Line 18: / Line 18: @@
 *I worked with my homework partner Dean Symonds [[MSymond1]] to complete this assignment. We worked together in class and texted once to ask a question. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 12:51, 31 January 2024 (PST)
-*I worked with my homework partner, Katie Miller, we texted briefly. We also worked together in class to choose the gene. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:47, 31 January 2024 (PST)
+*I worked with my homework partner, Katie Miller, we texted briefly. We also worked together in class to choose the gene. The picture of the structure was obtained using Jmol4 [https://proteopedia.org/wiki/fgij/fg.htm?mol=/wiki/fgijDATA/b6383740d762c5f8f62ee6d52dcd2efc/data.pdb link] Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:47, 31 January 2024 (PST)
 ===References===
 *LMU BioDb 2024. (2024). Week 3. Retrieved January 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_3

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 #*SGD:S000005476 [https://www.yeastgenome.org/locus/S000005476 SGD Page]
 #*NIH:854033 [https://www.ncbi.nlm.nih.gov/gene/854033 NIH Page]
-#*Ensemble: no page found for this gene
+#*Ensembl:P22148 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YOL116W;r=XV:99809-100957;t=YOL116W_mRNA Ensembl page]
 #*UniProt:P22148 [https://www.uniprot.org/uniprotkb/P22148/entry Uniprot Page]
 #DNA sequence [[image:MSN1sequence.png|200px]]

@@ Line 18: / Line 18: @@
 *I worked with my homework partner Dean Symonds [[MSymond1]] to complete this assignment. We worked together in class and texted once to ask a question. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 12:51, 31 January 2024 (PST)
-*The two homework partners, Katie and Dean, utilized each other for this assignment. They worked together in class for the assignment. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:47, 31 January 2024 (PST)
+*I worked with my homework partner, Katie Miller, we texted briefly. We also worked together in class to choose the gene. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:47, 31 January 2024 (PST)
 ===References===
 *LMU BioDb 2024. (2024). Week 3. Retrieved January 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_3