Hivanson and Nstojan1 Week 3

IMD3

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)?
  • SGD:
  • NCBI Gene Database:
  • Ensembl:
  • UniProt:
• What is the DNA sequence of your gene?
  • ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

• What is the protein sequence corresponding to your gene?

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 the rate-limiting step in the de novo synthesis of GTP and its involved in GTP biosynthesis pathways. In addition, it catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP). It is also known to play an important roll 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. e!Ensemble contains generic information that just covers the basics such as a name, description and type.
  • Were there differences in content, the information or data itself?
    • There were some differences in content, e!Ensemble didn’t really provide any information on the gene that would help one learn about it. On the other hand UniProt has a lot of information that could be useful for a person studying the gene.
  • Were there differences in presentation of the information?
    • 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.
• 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!)