Replaces accession AW018199
Blastx results: Many good hits with sequences annotated asretrotransposon. Highest hits are with sequences annotated in Cinfulfamily. Cinful protease-pol fusion protein:
gi|4206306|gb|AAD11615.1| prpol [Zea mays] 441 2e-122
gi|18568275|gb|AAL76007.1| prpol [Zea mays] 432 7e-120
gi|4206309|gb|AAD11616.1| prpol [Zea mays] 425 9e-118
gi|18254415|gb|AAL66756.1| putative prpol [Zea mays] 280 4e-74
gi|4680208|gb|AAD27571.1| polyprotein [Sorghum bicolor] >gi|4... 265 9e-70
BlastN supports blastx:
>gi|4206305|gb|AF049110.1| Zea mays retrotransposon Cinful-1, complete sequence
Length=8581
Score = 1053 bits (531), Expect = 0.0
Identities = 653/691 (94%), Gaps = 2/691 (0%)
Strand=Plus/Minus
Repeatmasker showed:
>DV489538 1000035-F04.T7-1 UGI-Reseq Zea mays cDNA, mRNA sequence. (690 bp masked -- 100.00% masked)
ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Repeats Blast showed best hits with:
>ZRSiTERTOOT0071 gi|4206305|gb|AF049110.1|AF049110 Zea mays
retrotransposon Cinful-1, complete sequence
Length = 8581
Score = 1053 bits (531), Expect = 0.0
Identities = 653/691 (94%), Gaps = 2/691 (0%)
Strand = Plus / Minus
Interpro scan showed best hits with:
noIPR
unintegrated
|
unintegrated
|
|
GENE3D
|
G3D.3.30.420.10
|
no description
|
4.6e-11 [123-222]T
|
|
PANTHER
|
PTHR10178
|
GAG/POL/ENV POLYPROTEIN
|
1.4e-49 [1-196]T
|
|
PANTHER
|
PTHR10178:SF14
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RETROVIRUS POLYPROTEIN
|
1.4e-49 [1-196]T
|
|
SUPERFAMILY
|
SSF56672
|
DNA/RNA polymerases
|
3.7e-12 [14-101]T
|
Parent no parent Children no children Found in no entries Contains no entries
Literature:
Gene loss and movement in the maize genome.Lai J,
Ma J,
Swigonova Z,
Ramakrishna W,
Linton E,
Llaca V,
Tanyolac B,
Park YJ,
Jeong OY,
Bennetzen JL,
Messing J.
Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA.
Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compared corresponding regions from sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum and maize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maize and sorghum approximately 50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excluding any transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the aligned regions are noncollinear between any two species. However, scoring each maize region separately, the set of noncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicated genes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5 million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomal positions, frequently in more than one. This demonstrates that many genes in these species have moved to new chromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically alter gene structure.
