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Final Predictions - Group 5

    7 confident predicted genes

     Our group's final presentation can be found here.

    7206-10856 Reverse Strand

    Exon 1:7421-7456

    Exon 2:7593-7721

    Exon 3:8031-8117

    Exon 4:8518-8583

    Exon 5:9922-10017

    Exon 6:10127-10243

    Predicted function:

     

    DNA-directed RNA polymerase II subunit I

     

    This is a strong prediction since it has a lot of hits when BLASTing against Arabidopsis, but also has a similar predicted function from the maize ESTs. 

    AGRY600_Gene1.jpg

     

    19047-25792 Forward Strand

    Exon 1: 19047-19196

    Exon 2: 19689-19918        

    Exon 3: 24884-24968        

    Exon 4: 25189-25272      

    Exon 5: 25364-25696        

    Exon 6: 25775-25792   

    Predicted function:

     

    Telomere repeat binding factor 2.

     

    While this is definitely a gene as there is strong support in all of the EST data, it is hard to make an exact predicted function.  However, all ESTs have something to do with DNA binding, so this gene most likely has a function in transcription regulation.  The shorter Augustus prediction is used since that is the version that has the most EST support.

    AGRY600_Gene2.jpg

     

    32825-35595 Reverse Strand

    Exon 1: 33353-33516

    Exon 2: 34458-34545

    Exon 3: 34619-34708

    Exon 4: 35008-35067

    Exon 5: 35143-35259

    Predicted function:

     

    While this gene in maize is completely uncharacterized, it shows homology to PUM1 in Arabidopsis, which functions in regulating both mRNA stability and translation through sequence specific binding to the 3’ UTR of target transcripts.  This was originally a predicted gene with low support, but thanks to strong EST data that agrees with both maize and Arabidopsis, we can be confident this is a gene.


    See EST BLASTs and final predictions here.

    AGRY600_Gene3.jpg

     

    101001-102816 Forward Strand

    Exon 1: 101001-101557

    Exon 2: 102747-102816

    Identified through AugustusFGENESH had same first exon but different second exon.  Did a blastp of both results and found better homology to Augustus result.

    Shows high homology to Sb03g026500 and Os01g0589700 with supporting EST data from Sorghum bicolor, Saccharum officinarium (sugar cane), and Zea mays. (Phytozome)  Plantgdb.org shows both EST and cDNA data supporting my gene structure.

    Splice donor site present after exon 1 and splice acceptor site found before exon 2. No polypyrimidine identified.

    AGRY600_Gene4.jpg

     

    107614-108618 Forward Strand

    Exon 1: 107614-108056

    Exon 2: 108504-108618

    Augustus and FGENESH showed gene structure exactly the same. Nucleotide blast (nr) showed a plant-light harvesting domain (PLN00014).

    Shows high homology to Sb03g026510 (2e-91) with supporting EST/cDNA data.  Also has supporting EST data from Saccharum officinarium (sugar cane) and Zea mays. (Phytozome) Maizegdb.org shows both EST and cDNA data supporting my gene structure.

    AGRY600_Gene5.jpg

     

    128236-128604 Forward Strand

    Exon 1: 128236-128365

    Exon 2: 128531-128604

    Augustus and FGENESH both show the same gene structure. Blastp of the proposed protein showed a top ofArabinogalactan peptide 22 from Arabidopsis (1e-06).  This is a relative high evalue but it did show a conserved domain of DUF1070.

    The DUF1070 is a family that consists of short hypothetical proteins of unknown function (http://aranet.mpimp-golm.mpg.de/pfamnet/DUF1070).  Gene ontolgy shows that the Arabinogalactan peptide 22 is a plasma membrane anchored protein (multiple GO terms) that appears to be involved in transport (GO:0006826 iron ion transport and GO:0015706 nitrate transport). It could also possibly be involved in brassinosteroid biosynthesis as proposed by gene ontology (GO:0016132). (http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q9FK16)

    AGRY600_Gene6.jpg

     

    143398-145767 (or 146054) Forward Strand

    Exon 1: 143398-143493

    Exon 2: 143562-143652

    Exon 3: 144047-144164

    Exon 4: 144238-144318

    Exon 5: 144399-144447

    Exon 6: 144715-144829

    Exon 7: 144945-145036

    Exon 8: 145136-145283

    Exon 9: 145743-145849

    Exon 10: 145881-146054

    Identified through both Augustus and FGENESH. Augustus has two possible gene structures (4 or 5 exons...additional internal exon). FGENESH has 11 exons. I believe FGENESH is more accurate according to EST/cDNA data (see below).

    Did a blastp and showed a hit on Serine/threonine-protein kinase (PKc_like superfamily domain) with an evalue of 5e-31 for transcript 1 from Augustus. Transcript 2 from augustus did not have as good of a match. FGENESH actually showed a stronger hit of 2e-138 (Serine/threonine-protein kinase AFC3). I therefore used the FGENESH and I tried to translate the EST data that showed Exon 3, 4, and 5 (or just 3 and 4 from cDNA/EST) being one exon and got stop codons.  The FGENESH also matched other cDNA/EST data where exon 3, 4, and 5 are separate.

    AGRY600_Gene7.jpg

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