BLASTn for original sequence produced the following top hits:
| Accession | Description | Max score | Total score | Query coverage | E value | Max ident | Links |
| AC138575.1 |
Zea mays genomic clone ZM16H10, finished contig 37381, complete sequence
|
1286 |
1286 |
100% |
0.0 |
98% |
|
| AY129008.1 |
Zea mays CRM centromeric retrotranposon, complete sequence
|
1284 |
1560 |
99% |
0.0 |
100% |
|
| AC138573.1 |
Zea mays genomic clone ZM16H10, finished contig 37379, complete sequence
|
449 |
449 |
33% |
7e-123 |
100% |
|
| AC138578.1 |
Zea mays genomic clone ZM16H10, finished contig 37606, complete sequence
|
427 |
427 |
31% |
3e-116 |
100% |
|
| AP008210.1 |
Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 4
|
320 |
1527 |
51% |
6e-84 |
90% |
|
| AL606447.3 |
Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBb0022F23, complete sequence
|
320 |
458 |
51% |
6e-84 |
87% |
BLASTx produced the followoing (nonsignificant) top hits:
Score E
Sequences producing significant alignments: (Bits) Value
gb|ABA93226.2| retrotransposon protein, putative, Ty3-gypsy s... 38.9 0.41
gb|ABB47096.2| retrotransposon protein, putative, Ty3-gypsy s... 37.4 1.2
gb|AAQ56336.1| putative polyprotein [Oryza sativa (japonica c... 37.4 1.2
The excellent BLASTn scores compared to the terrible BLASTx scores could suggest that this is a retrotranspson.
Repeatmasker results from MAGI database:
>DV491452 1000033-D10.T7-1 UGI-Reseq Zea mays cDNA, mRNA sequence. [MASKED: 726 bp (100.00%)]
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BLAST of MAGI's Repeats database:
Score E
Sequences producing significant alignments: (bits) Value
ZRSiCMCMOOT0036 gi|22296821|gb|AY129008.1| Zea mays CRM centrome... 1271 0.0
ORSiCMCM0010007 gi|3327953|gb|AF058904.1|AF058904 Oryza sativa s... 94 3e-19
HRSiTERTOOT0001 gi|4456993|gb|AF078801.1|AF078801|1809-11636 Hor... 52 1e-06
ORSiCMCMOOT0002 gi|5230421|gb|AF091233.1|AF091233 Oryza sativa s... 46 6e-05
RIRE7#LTR/gypsy 7403bp LTR 777bp no TR ASSEMBLE 7403 June 11, 20... 46 6e-05
gnl|TREP|TREP99 retrotransposon, LTR, gypsy, "Cereba_AY040832-2"... 44 2e-04
HRSiTERT0020015 gi|15340826|gb|AY040832.1| Hordeum vulgare Ty3/g... 44 2e-04
HRSiTERT0020014 gi|15340829|gb|AY040833.1| Hordeum vulgare Ty3/g... 44 2e-04
ZRSiTERTOOT0090 gi|3694836|gb|AF078917.1|AF078917 Zea mays centr... 42 0.001
Highest (excellent) hit when accession's sequence was used as a query of the repeat database at MAGI is as follows:
Sequences producing significant alignments: (bits) Value
ZRSiCMCMOOT0036 gi|22296821|gb|AY129008.1| Zea mays CRM cen... 1245 0.0
ORSiCMCM0010007 gi|3327953|gb|AF058904.1|AF058904 Oryza sat... 94 3e-19
HRSiTERTOOT0001 gi|4456993|gb|AF078801.1|AF078801|1809-1163... 52 9e-07
>ZRSiCMCMOOT0036 gi|22296821|gb|AY129008.1| Zea mays CRM centromeric
retrotranposon, complete sequence
Length = 7572
Score = 1271 bits (641), Expect = 0.0
Identities = 684/698 (97%), Gaps = 2/698 (0%)
Strand = Plus / Minus
Literature
Centromeric retroelements and satellites interact with maize kinetochore protein CENH3.
Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK.
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
Maize centromeres are composed of CentC tandem repeat arrays, centromeric retrotransposons (CRs), and a variety of other repeats. One particularly well-conserved CR element, CRM, occurs primarily as complete and uninterrupted elements and is interspersed thoroughly with CentC at the light microscopic level. To determine if these major centromeric DNAs are part of the functional centromere/kinetochore complex, we generated antiserum to maize centromeric histone H3 (CENH3). CENH3, a highly conserved protein that replaces histone H3 in centromeres, is thought to recruit many of the proteins required for chromosome movement. CENH3 is present throughout the cell cycle and colocalizes with the kinetochore protein CENPC in meiotic cells. Chromatin immunoprecipitation demonstrates that CentC and CRM interact specifically with CENH3, whereas knob repeats and Tekay retroelements do not. Approximately 38 and 33% of CentC and CRM are precipitated in the chromatin immunoprecipitation assay, consistent with data showing that much, but not all, of CENH3 colocalizes with CentC.