Hivanson and Nstojan1 Week 3

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IMD3

Summary of IMD3:

S. cerevisiae IMD3 is an Inosine-5′-monophosphate dehydrogenase (IMPDH) gene that is responsible for the catalysis of the rate-limiting step in de novo GTP synthesis. IMD3 is found in the cytoplasm of yeast cells and can bind metal ions, NAD, potassium, mRNA, and proteins. The function of IMD3’s mRNA binding capability is not known. The human orthologue of this gene is implicated in retinitis pigmentosa, a disease that causes blindness.

Other Information:

  • What is the standard name, systematic name, and name description for your gene (from SGD)?
    • Standard name: IMD3
    • Systematic name: YLR432W
    • Name description: IMP Dehydrogenase
  • What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
  • What is the DNA sequence of your gene?
    • ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA
  • What is the protein sequence corresponding to your gene?

IMD3 ExPasy.png

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF RTASAQLEGGVHNLHSYEKRLHN-

  • What is the function of your gene?
    • The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate (IMP) to xanthosine 5’-phosphate (XMP) during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
  • What was different about the information provided about your gene in each of the parent databases?
    • SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
    • There were some differences in content; Ensembl and NCBI didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt and SGD have a lot of information that could be useful for a person studying IMD3 and its functions.
    • Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary. Notably, SGD had a fun visual for comparative information and UniProt had an equally fun visual to show the subcellular location of IMD3. While all sites were navigable, some were more user-friendly than others; UniProt was outstanding in this with an attractive and intuitive UI while Ensembl was lacking.
  • Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
    • Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
  • Include an image related to your gene (be careful that you do not violate any copyright restrictions!)

Firstglance imd3.png

Acknowledgments

Natalija and Hailey worked together on the IMD3 “My Favorite Gene” journal entry. We split up the work evenly based on what we felt most comfortable answering and helped each other throughout our working on the page at the end of class on 1/30/24 and via text on 1/31/24.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Hivanson (talk) 22:16, 31 January 2024 (PST)

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Nstojan1 (talk) 08:01, 1 February 2024 (PST)

References

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