Putative Identification: Transoposon similar to Z. mays Activator Position: 26833 to 29405 Strand: - EST match: none Database match: sequence from Chr. IV, Z. mays Activator transposon
Analysis of the 2.6 kb region of BAC T32N15 from position 26833 to 29405 yields significant homology to a segment of the long arm of chromosome IV (Z97343) for which no genetic elements are defined. Thoroughout this region of T32N15 there is significant homology to transposable element Activator (Ac, X05424) of Zea mays and the Activator-like transposon of pearl millet (U02300). Also within this region is a 1.2 kb segment that forms an inverted repeat (T32N15 inverted repeat 2). In maize, the Ac transposon exhibits a conserved structure at each terminus: 11-bp inverted repeats define the ends of the transposon and these are flanked by 8-bp direct repeats. No such inverted repeats are found in this region of T32N15. This region does contain 11- and 12-bp inverted repeats of different sequence, but these themselves are not flanked directly but 8-bp direct repeats.
Comparison to Z. mays Activator transposon
A portion of exon 3 of Z. mays Activator exhibits
marked similarity to the polypeptide encoded by two exons, one
predicted by Grail (29405 to 29189) the other predicted by MZEF
(28916 to 28586). Over this range, the two sequences are 37%
identical and 51% similar. Other exons predicted by these two
programs cannot be incorporated into a larger polypeptide. It is
unclear whether this Activator-like transposon is complete or
functional, or whether it is disrupted by the neighboring
del-like transposon. Shown is an alignment of the polypeptide
encoded by two T32N15 exons (top) to the peptide sequence encoded
by exon 3 of Z. mays Activator (bottom).
. . . . .
1 ................TITTYFLGVKYPTANVYFLQVWKIERLLKDYAVC 34
:| | .| |||.:: .|. |: : |
501 EWKMALTLFKCLKKFFDLTELLSGTQYSTANLFYKGFCEIKDLIDQWCVH 550
. . . . .
35 GDLRVEEMASRMQVKFDKYWDQYNIILAIGAILDPRLKDV.......... 74
: || | ||:||| || ||: |||| | :
551 EKFVIRRMAVAMSEKFEKYWKVSNIALAVACFLDPRYKKILIEFYMKKFH 600
. . . . .
75 ..................FELERSIQPGSDNTKS................ 90
:: | | . ||.
601 GDSYKVHVDDFVRVIRKLYQFYSSCSPSAPKTKTTTNDSMDDTLMENEDD 650
. . . . .
91 NLQNYL.........DDPRLD.......LRSFTDMEVLSYWKGDGQRYGD 124
|||| : || |: ::||:|:| |
651 EFQNYLHELKDYDQVESNELDKYMSEPLLKHSGQFDILSWWRGRVAEYPI 700
. . . . .
125 LASLASAILSIPITTVAAESSFSIGGRVLNPFRNRILPRNVQALLCTRNW 174
| :| :|.| :.|||.||.|| ||||..|:|||: |:||:||:.|
701 LTQIARDVLAIQVSTVASESAFSAGGRVVDPYRNRLGSEIVEALICTKDW 750
. . . . .
175 LRGFAELE.......................................... 182
. .
751 VAASRKGATYFPTMIGDLEVLDSVIAAATNHENHMDEDEDAIEFSKNNED 800
Comparison to A. thaliana chromosome IV sequence Z97343. Z97343 is on the top; T32N15 is on the bottom.
. . . . .
160388 ATAGAGATGTTGTGGTGGGTAAAAAAGCCCAGCCCGACCTGAACCCAAAA 160437
||||||||| ||||||||||||||||||||||||||||||||||||||||
26833 atagagatgatgtggtgggtaaaaaagcccagcccgacctgaacccaaaa 26882
. . . . .
160438 TAAACCCGCCCACCAAAAACTCAACTTTAGAAAACCCAAATGGGTTTTTG 160487
||||| || |||||||||||||||||||||||||||| |||||||||||
26883 taaactcgttcaccaaaaactcaactttagaaaacccagatgggtttttg 26932
. . . . .
160488 ATTAGTGGGTAAAGCCCGAAAAAAACCTGATTGTTCTGATACTACCCGTG 160537
||| || || | ||||||| | |||| ||| || ||||||||||
26933 atttagtgggtaaaagccaaaaaaaaccgattattccgagactacccgtg 26982
. . . . .
160538 GGTACCCAACTTGATTTTTGTCTTTTTTTCTAGTGTTTATGTTTAATTAC 160587
||||||||||||| ||| |||| |||| | |||||||||||||||| | |
26983 ggtacccaacttggtttatgtcattttct.tagtgtttatgtttaactgc 27031
. . . . .
160588 TAATATACTATTATATATATTTTATATCTATATTTTGCTTATAAACTAAA 160637
|||||||||||||||| ||| || ||||||||||||||||||||| |||
27032 taatatactattatatgtatgttgtatctatattttgcttataaagtaag 27081
. . . . .
160638 CTGGTATGTAAATATATCATGTAAATTT.TTTTCATAGCAAAATAATAAT 160686
|||||||||||||||||||||||||||| ||| | |||||||||||||
27082 ctggtatgtaaatatatcatgtaaatttcgttttactgcaaaataataat 27131
. . . . .
160687 AATTTGTATGTCAAATTAAACAAGAAAAACTTAAAAAGTAATCAAATATC 160736
||||||||| ||||| ||||||||| |||||||||||||||||||| |||
27132 aatttgtatttcaaagtaaacaagagaaacttaaaaagtaatcaaaaatc 27181
. . . . .
160737 TGAAAATCAATTTAAAACAAAAAT.......................... 160760
|||||||||||||||||| ||||
27182 tgaaaatcaatttaaaactgaaatacaaaagtagttgaaaaaaaatctaa 27231
. . . . .
160761 ACAACATCTTCTCATACTCCAGAGCTACTTGCTACCGATGTAGTACCTTC 160810
|||||||||||||||||||||||| ||||||||| |||||||||||||||
27232 acaacatcttctcatactccagaggtacttgctatcgatgtagtaccttc 27281
. . . . .
160811 AATTCCATCATCAAAGTATTCTTCAATGTCACCTACAATTAGAAGATATA 160860
||||||||||| ||||| |||||||||||||||||||| |||||||||||
27282 aattccatcattaaagttttcttcaatgtcacctacaagtagaagatata 27331
. . .
160861 AATCAACAAATGAAAAAAAATTAAGTCCAAAAAA 160894
||||||||||| |||||||||||||| ||||||
27332 aatcaacaaataaaaaaaaattaagtataaaaaa 27365
{Inverted repeat 2 found here; see below.}
. . . . .
160889 AAAAAATTAGACTATTCTTTTTTTATCTTCCAACTCTGCAAAACCACGCA 160938
|||||| |||||||||||||||||| ||||||||||||||||||||||||
28560 aaaaaaatagactattctttttttaccttccaactctgcaaaaccacgca 28609
. . . . .
160939 ACGAGTTCCTAGTACATAACAAGGCTTGAACATTTCTCGGAAGAAGGCGG 160988
|| | || ||||||||||||||||||||||||||||| ||||||| ||||
28610 accaatttctagtacataacaaggcttgaacatttctgggaagaatgcgg 28659
. . . . .
160989 TTTCTGAAAGGGTTTAAAACCCGACCTCCAATACTGAATGATGACTCAGC 161038
||||||||||||||||||||||||||||||||||||||||||||||||||
28660 tttctgaaagggtttaaaacccgacctccaatactgaatgatgactcagc 28709
. . . . .
161039 TGCCACCGTAGTGATTGGAATGCTAAGTATAGCAGAAGCTAGAGAAGCTA 161088
|||||| |||||||||||||||||||||||||||||||||||||||||||
28710 tgccactgtagtgattggaatgctaagtatagcagaagctagagaagcta 28759
. . . . .
161089 AATCACCATAGCGTTGCCCATCGCCTTTCCAATAGCTTAGAACCTCCATG 161138
|||||||||| |||||||||||||||||||||||||| ||||||||||||
28760 aatcaccatatcgttgcccatcgcctttccaatagctcagaacctccatg 28809
161139 TTTGT 161143
| |||
28810 tctgt 28814
Inverted repeat 2:
The sequence from positions 27366 to 27732 (copy A) and from 28198 to 28559 (copy B) comprise a long, imperfect inverted repeat. The region that forms this inverted repeat disrupts a region that shows very strong identity to a segment from the long arm of chromosome IV, as outlined above. This inverted repeat can be divided into two regions, as shown below. The longer of these shares 88% sequence identitiy; the shorter has 76% identity.
. . . . .
27366 atgggaaaaatgtcaaaaaaatcgcgaactttcaaatttgggacgaaaaa 27415
||| |||||||||||||||||||| ||| |||||||||||||||| ||||
28559 atgagaaaaatgtcaaaaaaatcgtgaattttcaaatttgggacgtaaaa 28510
. . . . .
27416 agtatgaagtttcaagaagacaattaaatcctaaagtttagtttgacttt 27465
| ||||| |||||| |||||| |||||||||||||||||||||||||||
28509 aacatgaactttcaaaaagacatttaaatcctaaagtttagtttgacttt 28460
. . . . .
27466 tgataaaataatcaaaaattgttgacttgaccatttagggcatgtcatta 27515
||||||||| ||||| ||||||||||| ||| ||||||| |||| |||
28459 tgataaaatgatcaagttttgttgacttggccaattagggcttgtcgtta 28410
. . . . .
27516 agtttccgtcaaccaaacaatcacggagttaactttccgttagaatctct 27565
||||| ||||||| |||||||||||| ||||||||| ||||||||||||
28409 agttttcgtcaacaaaacaatcacggtgttaacttttcgttagaatctcc 28360
. . . .
27566 cttatatcaaaacgacgtcgttttgaaaattagaaaatgagaaagaaaa 27614
| | ||||||||| |||||||| | | |||||||||| |||| |||||
28359 gtgaaatcaaaacgccgtcgtttaggacattagaaaataagaaggaaaa 28311
. . . . .
27639 gaatcgaaatgctgacattctggactaatagaggatattcaaccattgag 27688
||| |||| |||||| || |||||| ||| || | ||||||||||||
28296 gaaacgaacagctgaccttttggacttataagagacactcaaccattgag 28247
. . . .
27689 ctgcattaacattttaatatctt.....acagacatagtatatatatat 27732
|| || ||| ||| | ||| | ||||| ||||||||||||
28246 ctacaataatattcttgtattatggtaaacagagcatgtatatatatat 28198
Summary:
Range Element
26833 to 27365 chromosome IV homology
27366 to 27732 inverted repeat 2, copy A
28198 to 28559 inverted repeat 2, copy B
28560 to 28814 chromsome IV homology
28586 to 28916 MZEF exon/Ac homology
29189 to 29405 Grail exon/Ac homology
created 26 Aug 97
Larry Parnell