Difference between revisions of "HSF1/YGL073W Week 3"
Jump to navigation
Jump to search
(pasted summary) |
(→References: added ExPasy reference) |
||
| (31 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
==Our Favorite Gene== | ==Our Favorite Gene== | ||
| − | + | HSF1/YGL073W | |
===Summary=== | ===Summary=== | ||
| Line 7: | Line 7: | ||
===Additional Information=== | ===Additional Information=== | ||
| − | # | + | #What is the standard name, systematic name, and name description for your gene (from SGD)? |
| − | #*Standard Name: | + | #*Standard Name: HSF1 |
| − | #*Systematic Name: | + | #*Systematic Name: YGL073W |
| − | #*Name Description: | + | #*Name Description: Heat Shock Transcription Factor |
| + | #What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)? | ||
| + | #*SGD: S000003041 [[https://www.yeastgenome.org/locus/S000003041 https://www.yeastgenome.org/locus/S000003041]] | ||
| + | #*NCBI: 3297 [[https://www.ncbi.nlm.nih.gov/gene/3297 https://www.ncbi.nlm.nih.gov/gene/3297]] | ||
| + | #*Ensembl: P10961 [[https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W_mRNA https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W_mRNA]] | ||
| + | #*UniProt: Q00613 [[https://www.uniprot.org/uniprot/Q00613 https://www.uniprot.org/uniprot/Q00613]] | ||
| + | #What is the DNA sequence of your gene? [https://www.ncbi.nlm.nih.gov/gene/852806/ NCBI] | ||
| + | #*ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGTATTGAGCCTT TACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGATATCTTTACGACCGATCGTAC CGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATTATTAACCCCTCATTGGATCCGCAGTCAGCA GCATCGCCGGTTCCTTCTTCCTCTTTTTTCCATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAA GGAGAGGTACTCCATTGGGAATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCC TAATAGTACATTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGCCAAACCACAA GAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGGAGCATGTTAAACGATGATTC TAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCTTTTATTGTCACGAATAGGGAGGAATTTGTG CACCAAATTTTACCAAAATATTTTAAACATTCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATG GATGGCATAAAGTTCAAGATGTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGA AAATGAAAACTTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGACAATGCCGCAG GAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAACAATGGTCATTTATTGCAGGG TAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGATAAGAATGATGTCACCGCGATTTTGGGGGAA TTAGAGCAAATAAAATATAACCAGATTGCAATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGT TATTATGGCAAGAGAATATGATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTT CAGATTCTTGACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGCACTATAGATG AACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACCAATGCTACAACCAACGCCCG TAATAACATGAGTCCCAACAATGATGACAATAGTATTGACACCGCTAGCACTAATACCACCAACAGAAAG AAAAATATAGATGAAAACATCAAAAATAACAACGACATAATTAATGACATTATATTTAATACCAACCTTG CCAACAATCTCAGCAATTACAATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATA TCTTTTGAAAAATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACGGATTTTAGGC CTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGATCCAAACAGATTTACGATGCT CTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGACAATAAACACAACGAAAGTGATCTTTTTTGG GACAACGTACATAGAAATATAGACGAACAAGATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATAC TTTCTCCTGGATATCCTAATAAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGA AAGTGCTGTCAACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAATGATAATGACA CCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTAACGCCCTTCCTCACGGTAGA TGATCACACACTAAACGACAATAACACTAGTGAGGGAAGTACAAGGGTGTCCCCCGATATAAAGTTCAGC GCCACTGAAAACACTAAAGTGAGTGATAACCTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCG ACACGGCGCCCGAGAACGCTAAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACA GGACCCGACAGAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAG | ||
| + | #What is the protein sequence corresponding to your gene? ([https://web.expasy.org/translate/ ExPASy tool]) [[Image:HSF1_amino_acid.png|1000 px|center]] | ||
| + | #What is the function of your gene? | ||
| + | #*The gene HSF1 is a transcription factor that activates specific genes which in turn promote the ability of Saccharomyces cerevisiae to maintain homeostasis when exposed to high temperature stressors. Its expression stimulates the further expression of heat shock proteins as well as chaperone proteins that maintain homeostasis despite suboptimal thermal conditions for the cells. | ||
| + | #What was different about the information provided about your gene in each of the parent databases? | ||
| + | #*SGD and Ensembl had matching summaries of HSF1. NCBI mentioned that it was a gene that regulated cell lifespan and is repressed by phosphorylation. UniProt focuses on its role as a chaperone protein during different types of cell stress as well as its effect on different mRNA molecules. | ||
| + | #*Were there differences in content, the information or data itself? | ||
| + | #**UniProt presented more details on the types and specific molecules HSF1 interacts with, but the other three databases were more generic and kept their summaries to the same length and information. | ||
| + | #*Were there differences in presentation of the information? | ||
| + | #**There were very few to no differences in the presentation of the information across the databases. Each one starts off with identification and summary of HSF1 and then goes into more and more details in an organized way. | ||
| + | #HSF1/YGL073W Image: ([https://pymol.org/2// PyMOL]) | ||
| + | [[Image: HSF1.PNG|500 px|center]] | ||
| + | |||
| + | ==Acknowledgments== | ||
| + | *We would like to acknowledge Dr. Dahlquist for her instruction on bioinformatics as well as her help with wiki formatting. | ||
| + | *We met with each other during class to discuss formatting and status of the wiki page. Other communication included answering questions on a shared Google Doc. | ||
| + | |||
| + | Except for what is noted above, this individual journal entry was completed by me and not copied from another source. | ||
| + | |||
| + | [[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 17:40, 16 September 2019 (PDT) | ||
| + | |||
| + | Except for what is noted above, this individual journal entry was completed by me and not copied from another source. | ||
| + | |||
| + | [[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 23:17, 16 September 2019 (PDT) | ||
| + | |||
| + | ==References== | ||
| + | Information of HSF1/YGL073 obtained from databases: | ||
| + | *HSF1/YGL073W Overview. (2019). Saccharomyces Genome Database. Retrieved from [[https://www.yeastgenome.org/locus/S000003041#resources https://www.yeastgenome.org/locus/S000003041#resources]]. | ||
| + | *HSF1 heat shock transcription factor 1 [Homo sapiens (humans)]. (2019). NCBI. Retrieved from [[https://www.ncbi.nlm.nih.gov/gene/3297 https://www.ncbi.nlm.nih.gov/gene/3297]]. | ||
| + | *Gene: HSF1 YGL073W. (2019). e!Ensembl. Retrieved from [[https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W_mRNA https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W_mRNA]]. | ||
| + | *Q00613 (HSF1_Human). (2019). UniProt. Retrieved from [[https://www.uniprot.org/uniprot/Q00613 https://www.uniprot.org/uniprot/Q00613]]. | ||
| + | *The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. | ||
| + | *ExPASy. (2019). Retrieved from [[https://web.expasy.org/translate/ https://web.expasy.org/translate/]] | ||
| + | Instructions for Week 3 assignment provided by LMU BioDB 2019. (2019). Week 3. Retrieved September 16, 2019, from [[https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_3]]. | ||
| + | |||
| + | |||
| + | |||
| + | [[Category:Journal Entry]] | ||
Latest revision as of 15:59, 17 September 2019
Our Favorite Gene
HSF1/YGL073W
Summary
HSF1/YGL073W is a gene that encodes for a transcription factor that regulates the cell’s response to stress. It is best studied for its response to high temperature. During high temperature stress, the gene allows for the transcription of the proteins that protect the cell from heat shock effects, such as denaturation of proteins or excess cell replication. The HSF1 protein also helps regulate transcription for the maintenance of cell wall structure, folding of proteins, and detoxification of cell impurifications. It does not induce transcription in unstressed cells, and it is located within the nucleus of the cell.
Additional Information
- What is the standard name, systematic name, and name description for your gene (from SGD)?
- Standard Name: HSF1
- Systematic Name: YGL073W
- Name Description: Heat Shock Transcription Factor
- What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
- SGD: S000003041 [https://www.yeastgenome.org/locus/S000003041]
- NCBI: 3297 [https://www.ncbi.nlm.nih.gov/gene/3297]
- Ensembl: P10961 [https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W_mRNA]
- UniProt: Q00613 [https://www.uniprot.org/uniprot/Q00613]
- What is the DNA sequence of your gene? NCBI
- ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGTATTGAGCCTT TACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGATATCTTTACGACCGATCGTAC CGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATTATTAACCCCTCATTGGATCCGCAGTCAGCA GCATCGCCGGTTCCTTCTTCCTCTTTTTTCCATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAA GGAGAGGTACTCCATTGGGAATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCC TAATAGTACATTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGCCAAACCACAA GAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGGAGCATGTTAAACGATGATTC TAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCTTTTATTGTCACGAATAGGGAGGAATTTGTG CACCAAATTTTACCAAAATATTTTAAACATTCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATG GATGGCATAAAGTTCAAGATGTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGA AAATGAAAACTTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGACAATGCCGCAG GAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAACAATGGTCATTTATTGCAGGG TAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGATAAGAATGATGTCACCGCGATTTTGGGGGAA TTAGAGCAAATAAAATATAACCAGATTGCAATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGT TATTATGGCAAGAGAATATGATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTT CAGATTCTTGACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGCACTATAGATG AACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACCAATGCTACAACCAACGCCCG TAATAACATGAGTCCCAACAATGATGACAATAGTATTGACACCGCTAGCACTAATACCACCAACAGAAAG AAAAATATAGATGAAAACATCAAAAATAACAACGACATAATTAATGACATTATATTTAATACCAACCTTG CCAACAATCTCAGCAATTACAATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATA TCTTTTGAAAAATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACGGATTTTAGGC CTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGATCCAAACAGATTTACGATGCT CTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGACAATAAACACAACGAAAGTGATCTTTTTTGG GACAACGTACATAGAAATATAGACGAACAAGATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATAC TTTCTCCTGGATATCCTAATAAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGA AAGTGCTGTCAACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAATGATAATGACA CCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTAACGCCCTTCCTCACGGTAGA TGATCACACACTAAACGACAATAACACTAGTGAGGGAAGTACAAGGGTGTCCCCCGATATAAAGTTCAGC GCCACTGAAAACACTAAAGTGAGTGATAACCTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCG ACACGGCGCCCGAGAACGCTAAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACA GGACCCGACAGAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAG
- What is the protein sequence corresponding to your gene? (ExPASy tool)
- What is the function of your gene?
- The gene HSF1 is a transcription factor that activates specific genes which in turn promote the ability of Saccharomyces cerevisiae to maintain homeostasis when exposed to high temperature stressors. Its expression stimulates the further expression of heat shock proteins as well as chaperone proteins that maintain homeostasis despite suboptimal thermal conditions for the cells.
- What was different about the information provided about your gene in each of the parent databases?
- SGD and Ensembl had matching summaries of HSF1. NCBI mentioned that it was a gene that regulated cell lifespan and is repressed by phosphorylation. UniProt focuses on its role as a chaperone protein during different types of cell stress as well as its effect on different mRNA molecules.
- Were there differences in content, the information or data itself?
- UniProt presented more details on the types and specific molecules HSF1 interacts with, but the other three databases were more generic and kept their summaries to the same length and information.
- Were there differences in presentation of the information?
- There were very few to no differences in the presentation of the information across the databases. Each one starts off with identification and summary of HSF1 and then goes into more and more details in an organized way.
- HSF1/YGL073W Image: (PyMOL)
Acknowledgments
- We would like to acknowledge Dr. Dahlquist for her instruction on bioinformatics as well as her help with wiki formatting.
- We met with each other during class to discuss formatting and status of the wiki page. Other communication included answering questions on a shared Google Doc.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Ymesfin (talk) 17:40, 16 September 2019 (PDT)
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Imacarae (talk) 23:17, 16 September 2019 (PDT)
References
Information of HSF1/YGL073 obtained from databases:
- HSF1/YGL073W Overview. (2019). Saccharomyces Genome Database. Retrieved from [https://www.yeastgenome.org/locus/S000003041#resources].
- HSF1 heat shock transcription factor 1 [Homo sapiens (humans)]. (2019). NCBI. Retrieved from [https://www.ncbi.nlm.nih.gov/gene/3297].
- Gene: HSF1 YGL073W. (2019). e!Ensembl. Retrieved from [https://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W_mRNA].
- Q00613 (HSF1_Human). (2019). UniProt. Retrieved from [https://www.uniprot.org/uniprot/Q00613].
- The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
- ExPASy. (2019). Retrieved from [https://web.expasy.org/translate/]
Instructions for Week 3 assignment provided by LMU BioDB 2019. (2019). Week 3. Retrieved September 16, 2019, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_3].
