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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttatattattaacctccaaatacagtcagtatgctctagtttaagttttggttttctacagcatgctgtggtcatttaatcatattgttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG

Basic information

species Zea mays
transcript GRMZM2G151268_T04
intron # 4
splice site 3'
intron type U2

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|22935937|gb|BU572212.1|BU572212
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|45847355|gb|CN071298.1|CN071298
EST:     TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGCCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|78122445|gb|DV540829.1|DV540829
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|29945213|gb|CB815527.1|CB815527
EST:     AAAGTGGTCCACTGCTTTTAGATGGTCTCGAAGGGTATCTGAAATATGAG                         AATTTGTCTCAAGCAAG
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAG
EST: gi|21432449|gb|BQ547939.1|BQ547939
EST:     AAAGTGGTCCCCTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60359679|gb|DN226652.1|DN226652
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|32864387|gb|CF004069.1|CF004069
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|23357627|gb|BU645276.1|BU645276
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60399944|gb|DN232751.1|DN232751
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|26557650|gb|CA829885.1|CA829885
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATTTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|21432197|gb|BQ547687.1|BQ547687
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|113701244|gb|EE678748.1|EE678748
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211194039|gb|FL029192.1|FL029192
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|89106102|gb|DY576319.1|DY576319
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|67042990|gb|CO469245.1|CO469245
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|29945211|gb|CB815526.1|CB815526
EST:     AAAGTGGTCCNCTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211191650|gb|FL029191.1|FL029191
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|26557724|gb|CA829959.1|CA829959
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttttggttttctacagcatgctgtggtcatttaatcatattgttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG
                               atttaat  putative branch site (score: 4)
                                          ttgtttt  putative PPT
                               atttaatcatattgtt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttatattattaacctccaaatacagtcagtatgctctagtttaagttttggttttctacagcatgctgtggtcatttaatcatattgttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG