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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagaagaggggggaaaacaatgtgacatactccccgagtagaacatataacctttttctcatcttattaattcgtatgtatgtatcactgtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAATTGCCAAGAGCCATGGCTTGAAGCTTCATATCGATGGAGCTCGCATCTTC

Basic information

species Zea mays
transcript GRMZM2G147256_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147256_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G08630.5 (Arabidopsis thaliana), 3'ss of exon 3
gaagaagaggggggaaaacaatgtgacatactccccgagtagaacatat----aacctttttctcatct-tattaattcgtatgtatgtatcactgtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAATTGCCAAGAGCCATGGCTTGAAGCTTCATATCGATGGAGCTCGCATCTTC
       | |  | |  |  |  |     |||     || ||| | |      ||   | | || || | | | |||        ||| | |  || |  |||||  ||||||| |  |||||    || ||||||||||| || ||||| || ||||| ||||| |||||| ||||||| |||||||| ||||| ||  | |||
-----gtacgatgaattattaaatatttgactgttaaagcagagcctcgttcgaatactatgcttatatgtgtcaataaacggccatgcacc--tgataatgcagCTCTGGTGGGAGATGTTTGAGCGTGGAATACACTGAGAAAGTTGGAGAGATTGCGAAGAGACATGGCGTGAAGCTCCATATCGACGGAGCCCGTCTTTTC
















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|50335428|gb|CO530554.1|CO530554
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|50323799|gb|CO518925.1|CO518925
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|453306|gb|T15280.1|T15280
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|94474056|gb|EB703014.1|EB703014
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|101397912|gb|EB820833.1|EB820833
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|71299598|gb|DR785812.1|DR785812
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|50336980|gb|CO532106.1|CO532106
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|71424593|gb|DR806375.1|DR806375
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|74236570|gb|DT644484.1|DT644484
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|31363479|gb|CD447836.1|CD447836
EST:     CTCCATTACCCGACGACCAGACTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTCAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|148945236|gb|EC890443.2|EC890443
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|93284472|gb|EB676736.1|EB676736
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|50335971|gb|CO531097.1|CO531097
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|76912289|gb|DV164659.1|DV164659
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|50330663|gb|CO525789.1|CO525789
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGT
EST: gi|78082345|gb|DV510757.1|DV510757
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|50334096|gb|CO529222.1|CO529222
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|71437980|gb|DR819030.1|DR819030
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|71448613|gb|DR829663.1|DR829663
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
EST: gi|71766307|gb|DR964244.1|DR964244
EST:     CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAA                         TACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT
genomic: CTCCATTACCCGACGACCAGATTGATCTGCTTGGAGAACACACATGGGAAgtgagttgca ... gtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataacctttttctcatcttattaattcgtatgtatgtatcactgtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAATTGCCAAGAGCCATGGCTTGAAGCTTCATATCGATGGAGCTCGCATCTTC
                    tattaat  putative branch site (score: 2)
                                           ctgtttct  putative PPT
              tcatcttattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagaagaggggggaaaacaatgtgacatactccccgagtagaacatataacctttttctcatcttattaattcgtatgtatgtatcactgtttctgcagTACTGGTGGAAAGTGTTTATCTGTAGAATACACTGACAAGGTTGGTGAAATTGCCAAGAGCCATGGCTTGAAGCTTCATATCGATGGAGCTCGCATCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
gaagaaga
- - - - - - - aaaacaa
- - - - - - - - - - - - - catactc
- - - - - - - - - - - - - - - - - - - - -gaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtatg