Cwong34 Week 14

Gene Database Information

The QA's met, and we chose which information we wanted to take from which databases.

NCBI

• Locus tag
  • YGL073W
• Gene ID
  • 852806
• Also known as
  • EXA3; MAS3

UniProt

• Protein type/name
  • Heat shock factor protein
• Species
  • Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Protein sequence
  • MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI

INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK

• Gene ID
  • P10961 (HSF_YEAST)
• Similar proteins & ID of similar protein
  • N1P1W2 - ID: P10961

Ensembl

• DNA sequence
  • >chromosome:R64-1-1:VII:368153:371854:1

AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC

• Gene description/function
  • Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]
• Gene ID
  • YGL073W
• Gene map
  • File:Saccharomycescerevisiae HSF1.pdf
• Gene location
  • Chromosome VII: 368,753-371,254

SGD

• Gene ID
  • S000003041
• Standard name
  • HSF1
• Systematic name YGL073W
• Gene regulation (Regulators & targets)
  • Regulators: 6
  • Targets: 478
• Total interactions
  • 85 total for 71 unique genes
• Physical interactions
  • Affinity Capture-MS: 11
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 4
  • Biochemical Activity: 11
  • Co-localization: 3
  • Reconstituted Complex: 2
  • Two-hybrid: 3
• Genetic interactions
  • Dosage Rescue: 16
  • Negative Genetic: 8
  • Phenotypic Suppression: 5
  • Synthetic Growth Defect: 2
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 6
  • Synthetic Rescue: 11
• Gene ontology
  • Summary: Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling
  • Molecular Function:
    • Manually Curated: DNA binding transcription factor activity (IDA)
    • High-Throughput: sequence-specific DNA binding (HDA)
  • Biological Process
    • Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)
  • Cellular Component
    • Manually Curated: nucleus (IDA)
  • High-Throughput: mitochondrion (HDA)

JASPAR

• Matrix ID
  • MA0319.1
• Class
  • Heat shock factors
• Sequence logo
  • Image below
• Frequency matrix
  • Image below

Getting Organized

• During class, I worked on our team page to map out our deliverables and milestones. I met with our team members to check in on how they are doing and to get a better idea of where our team is in our project.
• I created the deliverables page for our team (Gene hAPI Deliverables)

Acknowledgments

1. I worked with the other QAs and Dr. Dahlquist to come up with a list of information to pull from the different databases.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Cwong34 (talk) 00:15, 5 December 2017 (PST)

References

1. LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14
• Week 15

Journal Entries:

• cwong34 Week 2
• cwong34 Week 3
• cwong34 Week 4
• cwong34 Week 5
• cwong34 Week 6
• cwong34 Week 7
• cwong34 Week 8
• cwong34 Week 9
• cwong34 Week 10
• cwong34 Week 11
• cwong34 Week 12
• cwong34 Week 14
• cwong34 Week 15

Shared Journals:

• cwong34 Week 1 Journal
• cwong34 Week 2 Journal
• cwong34 Week 3 Journal
• cwong34 Week 4 Journal
• cwong34 Week 5 Journal
• cwong34 Week 6 Journal
• cwong34 Week 7 Journal
• cwong34 Week 8 Journal
• cwong34 Week 9 Journal
• cwong34 Week 10 Journal

Group Project

• Gene hAPI
• Gene hAPI Deliverables