Replaces accession AI737422

No longer sequences were available.                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|99866732|gb|ABF67945.1|  putative Opie4 gag protein [Zea mays]  399    7e-110
gi|17082480|gb|AAL35397.1|  Opie2b gag protein [Zea mays]          395    1e-108
gi|33113970|gb|AAP94592.1|  retrotransposon Opie-2 [Zea mays]      393    5e-108
gi|99866719|gb|ABF67933.1|  Opie3 gag protein [Zea mays]           389    5e-107
gi|99866697|gb|ABF67913.1|  Opie2 gag protein [Zea mays]           386    4e-106
gi|18254418|gb|AAL66759.1|AF464738_10  putative pol protein [Zea   382    1e-104
gi|4185310|gb|AAD09017.1|  gag protein [Zea mays]                  380    3e-104
gi|17082478|gb|AAL35395.1|  Opie2a gag protein [Zea mays]          377    3e-103
gi|3645898|gb|AAC49501.1|  Gag [Zea mays]                          373    4e-102
gi|18254419|gb|AAL66760.1|AF464738_11  putative gag protein [Zea   337    4e-91
gi|74476706|gb|ABA08421.1|  Gag [Zea mays]                         308    2e-82
gi|18542174|gb|AAL75483.1|AF466202_9  putative pol protein [Zea m  285    2e-75

BLASTn of sequence:

InterPro Scan of sequence:

SEQUENCE: DV492877_5_ORF1 CRC64: 9805200973018FF4 LENGTH: 224 aa
InterPro IPR001878 Domain	Zinc finger, CCHC-type PRINTS PR00939 C2HCZNFINGER 2.2 [135-144]T 2.2 [144-152]T PFAM PF00098 zf-CCHC 1.7e-06 [135-152]T SMART SM00343 ZnF_C2HC 0.00023 [136-152]T PROFILE PS50158 ZF_CCHC 10.263 [137-152]T
Parent	no parent
Children	no children
Found in	IPR015466
Contains	no entries
GO terms	Molecular Function: nucleic acid binding (GO:0003676) Molecular Function: zinc ion binding (GO:0008270)

Related Literature:

Special Feature
Plant Biology
Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus

( variability | helitrons | retrotransposons | corn )

Qinghua Wang * and Hugo K. Dooner *

^*The Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08855; and Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901

Edited by Susan R. Wessler, University of Georgia, Athens, GA, and approved August 1, 2006 (received for review April 17, 2006)

Maize is probably the most diverse of all crop species. Unexpectedly large differences among haplotypes were first revealed in a comparison of the bz genomic regions of two different inbred lines, McC and B73. Retrotransposon clusters, which comprise most of the repetitive DNA in maize, varied markedly in makeup, and location relative to the genes in the region and genic sequences, later shown to be carried by two helitron transposons, also differed between the inbreds. Thus, the allelic bz regions of these Corn Belt inbreds shared only a minority of the total sequence. To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the bz genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. This vertical comparison has revealed the existence of several new helitrons, new retrotransposons, members of every superfamily of DNA transposons, numerous miniature elements, and novel insertions flanked at either end by TA repeats, which we call TAFTs (TA-flanked transposons). The extent of variation in the region is remarkable. In pairwise comparisons of eight bz haplotypes, the percentage of shared sequences ranges from 25% to 84%. Chimeric haplotypes were identified that combine retrotransposon clusters found in different haplotypes. We propose that recombination in the common gene space greatly amplifies the variability produced by the retrotransposition explosion in the maize ancestry, creating the heterogeneity in genome organization found in modern maize.

Author contributions: H.K.D. designed research; Q.W. performed research; Q.W. and H.K.D. analyzed data; and H.K.D. wrote the paper.