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Several families of maize gene-enriched sequences have been produced (AZM,EST,MSLL,HMPR), and
maize is currently undergoing full BAC-by-BAC sequencing. We download the most current maize BACs
from Genbank every night and align the gene-rich sequences to them, in order to
elucidate their structure.
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This site has been funded in part by
NSF grant #0321724
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| Mini-BACs
| A table of images showing the gene evidence for each BAC, with links to the genome browser.
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| BLAST
| Blast your sequence to the maize gene rich sequences
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| Contig Extensions
| View sequence upstream and downstream of EST contigs |
| Order
| Many of the clones for the gene rich sequences may be ordered.
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Mini-BACs: A table of images that show a birds-eye view of MSLL and HMPR[1],
AZMs[2], EST contigs[3],
and repeats along the maize BACs[4]. These are updated regularly with new and updated
sequenced BACs from Genbank. Each BAC image links to a Genome Browser of the BAC with
additional tracks for Methyl-filtered, High-Cot, RescueMU[5], BESs[6], and FGENESH[7]
predictions.
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BLAST: The gene rich sequences are MSLL, HMPR, AZM, RescueMU, and EST contigs.
Each resulting alignment links to the Genome Browser showing its location.
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Contig Extensions: The MSLL, HMPR and AZM sequences have been aligned to the ends of
the maize EST contigs to provide extensions.
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Orders: The Arizona Genome Institute provides the clones for MSLL, HMPR, ESTs from the Maize FL-cDNA project, and the MF and HC from the AZM project [2].
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[1]
MSLL and HMPR
Nelson, W., Luo, M., Ma, J., Haller, K., Bharti, A., Messing, J., Wing, R., San Miguel, P., Bennetzen, J., and Soderlund, C. (in preparation).
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[2]
Assembled Zea Mays (Methyl-Filtered and High Cot sequence)
Whitelaw, C.A., Barbazuk, W.B., Pertea, G., Chan, A.P., Cheung, F., Lee, Y., Zheng, L., van Heering
en, S., Karamycheva, S., Bennetzen, J.L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman,
M.A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy,
R., Fraser, C.M., and Quackenbush, J. (2003). Enrichment of gene-coding sequences in maize by genome filtration.
Science 302, 2118-2120.
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[3] Maize FL-cDNA Project
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[4] Maize Sequencing Project
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[5] RescueMU Project
Fernandes, J., Dong, Q., Schneider, B., Morrow, D., Nan, G., Brendel, V., and Walbot, V. (2004). Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biology 5: R82.
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[6] Maize BES sequences
Messing, J., Bharti, A.K., Karlowski, W.M., Gundlach, H., Kim, H.R., Yu, Y., Wei, F., Fuks, G., Soderlund, C., Mayer, K.F.X. and Wing, R.A. (2004) Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101: 14349-14354.
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[7] Fgenesh gene finding program (Salamov and Solovyev)
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