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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaataaacttccaaaaactaaggattagatatttaatatgaccataaatttcactgtttgttctaactcttgtaactgatgtgggatttctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCTATATGTGTGGACATCACCGACAACGAATTGGCATACTTGGAATGTATCC

Basic information

species Zea mays
transcript GRMZM2G052713_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
-agtaataaacttccaaaaactaaggattagatatttaatatgaccataaatttcactgtttgttctaactcttgtaactgatgtgggatttctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCTATATGTGTGGACATCACCGACAACGAATTGGCATACTTGGAATGTATCC
   |   |   |    ||   | |  ||   |  | | | |  |   |    |  | ||    |    |   |         ||||  | || ||||||||||||| ||||| ||||||||||| ||| ||||||||||||| |||||||| || |||||||| ||||| ||||| || ||||||||||||||||| ||||
tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggtata-tgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60352004|gb|DN218977.1|DN218977
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344140|gb|FL188310.1|FL188310
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344147|gb|FL188317.1|FL188317
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACMAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTYCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|32938017|gb|CF042836.1|CF042836
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344138|gb|FL188308.1|FL188308
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|60394275|gb|DN227145.1|DN227145
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|67011386|gb|CO440135.1|CO440135
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|32936019|gb|CF040831.1|CF040831
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344136|gb|FL188306.1|FL188306
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344143|gb|FL188313.1|FL188313
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344148|gb|FL188318.1|FL188318
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|60351820|gb|DN218793.1|DN218793
EST:     GCATCNGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: GCATC-GGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344139|gb|FL188309.1|FL188309
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|60356394|gb|DN223367.1|DN223367
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344141|gb|FL188311.1|FL188311
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211341753|gb|FL188303.1|FL188303
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT
EST: gi|211344137|gb|FL188307.1|FL188307
EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatttcactgtttgttctaactcttgtaactgatgtgggatttctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCTATATGTGTGGACATCACCGACAACGAATTGGCATACTTGGAATGTATCC
                                           tttctcat  CT-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaataaacttccaaaaactaaggattagatatttaatatgaccataaatttcactgtttgttctaactcttgtaactgatgtgggatttctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCTATATGTGTGGACATCACCGACAACGAATTGGCATACTTGGAATGTATCC

- - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ttcactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt