Difference between revisions of "Malcolm C"

Revision as of 19:18, 12 April 2012

This is where I will capture my progress on this project.

I will also be working on the 13 genes Allan gave us.

The class has already completed 4 SSR primer designs (LDOX, CHS, StSy, and F3H).

Results from Blueberry 454 Scaffold Searches from Grape (given to us by Allan Brown)
AOMT Scaffold 00796

1. Forward Primer GAGCTCTTGGATGCTCCATACT & Rev Primer CCTCATAATTTTTGGTCTTCGC (taa) x6 PCR product = 137 bp
2. Forward Primer TATCCCATGTTTTGGCTAATCC & Rev Primer TTTGCTTTTCAATCGGGAAC (tc) x9 PCR product = 261 bp

AOMT scaffold 01781

1. Forward Primer GGCGACTGTGTCTTTCAGTAAA & Rev Primer TAGGATTTCGAGGAGGAGAGGT (ct) x7 PCR product = 136 bp
2. Forward Primer ATAAACAGGTAAACCGAACCGA & Rev Primer CCGATTAAATTGGAGCAGTAGC (tg) x7 PCR product = 262 bp

ANPER scaffold 00666

1. Forward Primer TTTCTATCTCTCTCGCCGTCAT & Rev Primer GTTTTCTCACCTTGTTTTTGCC (ct) x21 PCR product = 219 bp
2. Forward Primer CCGTTTCGATCTCTCTCTCAGT & Rev Primer CATCCCTAGATCTGACACCACA (tc) x14 PCR product = 278 bp

CHI scaffold 03186

1. Forward Primer TACATCTTGAGGGGCAGTTTTT & Rev Primer GTGGAGTGTGGGATATGGATTT (tc) x5 PCR product = 121 bp
2. Forward Primer ACGTGGTCCAATCTAACCTCAC & Rev Primer TAGTAAGTGGAGGCCGGTAAAA (cttt) x4 PCR product = 288 bp

DFR scaffold 03132

1. Forward Primer TACATCTTGAGGGGCAGTTTTT & Rev Primer GTGGAGTGTGGGATATGGATTT (tc) x5 PCR product = 121 bp
2. Forward Primer ACGTGGTCCAATCTAACCTCAC & Rev Primer TAGTAAGTGGAGGCCGGTAAAA (cttt) x4 PCR product = 288 bp

F3'H scaffold 01438

1. Forward Primer CAGTGGTACAGTGGTGGATGAC & Rev Primer ATTCCCTTTCTCTTCCCATTTC (ag) x7 PCR product = 152 bp
2. Forward Primer ATACCAATCCATAGTCTCCCGA & Rev Primer TCAGTTGTGTTTTTCAGTTGGG (ta) x7 PCR product = 279 bp

FLS scaffold 00142

1. Forward Primer CAATTATACCCTTCCTGTCCCA & Rev Primer GAATGGATGAAAGGAACCCATA (ag) x8 PCR product = 214 bp
2. Forward Primer CTAGCTCTCCCTCTCTCCCTCT & Rev Primer GTGGTACTCCATATCCATGCCT (ct) x8 PCR product = 295 bp

FLS scaffold 00374

1. Forward Primer TGAGCATCATTGCCAGAGTAGT & Rev Primer GGATTTCATTCCAAGAGATTGC (ct) x6 PCR product = 295 bp
2. Forward Primer TAGATTATCCGGGGAATCATTG & Rev Primer GATTCTCATGACAAGCCAGTTG (tc) x6 PCR product = 275 bp

MYBA1 scaffold 03500

1. Forward Primer GCGAGGATGGAAATATATACGG & Rev Primer GCTTCATAAGCTGCTAGGCAAT (ag) x8 PCR product = 222 bp
2. Forward Primer GCGAGGATGGAAATATATACGG & Rev Primer GCTTCATAAGCTGCTAGGCAAT (ttat) x5 PCR product = 222 bp

MYCA1 scaffold 00278

1. Forward Primer CAGTATTTGAGCCGGAACCTAC & Rev Primer CGTACAGAGTTTCGCACAAAAG (ct) x7 PCR product = 268 bp
2. Forward Primer TAGTGGGAACGAGTCGTCTTTT & Rev Primer AGTTGGTGCCCTTTTATGAAGA (at) x6 PCR product = 195 bp

MYCA1 scaffold 00554

1. Forward Primer GGCTAAAACCCTAGTTGCCTTT & Rev Primer GGGTGTACTGAGAACCGAAGTC (tc) x6 PCR product = 157 bp
2. Forward Primer CCCAAAAGAAAATACCTGGACA & Rev Primer GGAGCTTGGACCTAAAAGGATT (ga) x8 PCR product = 260 bp

UFGT scaffold 00304

1. Forward Primer TGAACTACCAAAATGGGACAGA & Rev Primer NGACGGAGCACATCCTACTACA (ag) x10 PCR product = 207 bp
2. Forward Primer CCCCAAATTCAGATCAAAGAAG & Rev Primer CTTATCTCTGCCCACCTACACC (ag) x12 PCR product = 230 bp

UFGT scaffold 01120

1. Forward Primer TGTGTGTGTGTAGTGTGGTCGT & Rev Primer AAGAGAGAGGGGTCCTGAAAAC (ct) x11 PCR product = 132 bp
2. Forward Primer TAAGCTACAGTACCTCGCCACA & Rev Primer AAGGATATGCCGACGAGTCTTA (tc) x6 PCR product = 196 bp

For the second half of the semester, we focused on finding ESTs of our genes using the Washington State University Vaccinium genome database as well as the Towson State University Blue Berry Genome database using 454 sequencing.