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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaatggattatgggcaaatggatttaagagtggttctgcgtgtcaacttccataggtttttatattcaatttacccccctcaaattcttgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCCTGCAACAAGAACGAGCAGCTGGCCGCCAACTACCTCTTGGATCACATGC

Basic information

species Zea mays
transcript GRMZM2G061620_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061620_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os09g24200.1 (Oryza sativa), 3'ss of exon 10
gtaagtcaatggattatggg----caaatgg---atttaagagtggttctgcgtgtcaacttccataggtttttatattcaatttacccccctcaaattcttgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCCTGCAACAAGAACGAGCAGCTGGCCGCCAACTACCTCTTGGATCACATGC
|| |||| |   ||   |      |  |||      |||   ||  |  ||| | |  | |        |    |||   |   || |  |||    |||   || |  |||||||||  |||||||||||||| || || || ||||| ||||||||||| ||||||||| ||||||||||||| || ||||| ||| | ||||||||| 
gtgagtcgaaaaatcccgaattcccctatgctctgcttagttgtcatcttgcttttagaatatttgctttacacataactagcataacatcctttctttcac-atcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA
















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|4804466|gb|AI665336.2|AI665336
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|33092724|gb|CF052718.1|CF052718
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|32944591|gb|CF049410.1|CF049410
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGA
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGA
EST: gi|88748485|gb|DY532626.1|DY532626
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTTTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211179390|gb|FL472344.1|FL472344
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|33103634|gb|CF063594.1|CF063594
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|60396214|gb|DN229083.1|DN229083
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|16922733|gb|BM075725.1|BM075725
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|33091188|gb|CF051182.1|CF051182
EST:     CACTCCAGAGGAGTGCGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211090633|gb|FK965684.1|FK965684
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211167569|gb|FL481155.1|FL481155
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|6431881|gb|AW172085.1|AW172085
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|101401580|gb|EB822466.1|EB822466
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAAGGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTTTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211510600|gb|FL470556.1|FL470556
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|16927288|gb|BM080357.1|BM080357
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|32850730|gb|CD990411.1|CD990411
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGNGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211460054|gb|FL445989.1|FL445989
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211460055|gb|FL445990.1|FL445990
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|33104092|gb|CF064052.1|CF064052
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTC--                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|16926213|gb|BM079281.1|BM079281
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|78073733|gb|DV502167.1|DV502167
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAAGGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTTTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|211501745|gb|FL041143.1|FL041143
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|78078954|gb|DV507366.1|DV507366
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTTTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|60355834|gb|DN222807.1|DN222807
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|60339280|gb|DN206253.1|DN206253
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTTTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|18173700|gb|BM349088.1|BM349088
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|76280697|gb|DV020265.1|DV020265
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|76288771|gb|DV028339.1|DV028339
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
EST: gi|4966941|gb|AI691754.1|AI691754
EST:     CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT                         CTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC
genomic: CAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGTgtaagtcaat ... tgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttccataggtttttatattcaatttacccccctcaaattcttgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCCTGCAACAAGAACGAGCAGCTGGCCGCCAACTACCTCTTGGATCACATGC
                                          tcttgat  putative branch site (score: 4)
                                         ttctt  CT-rich tract
        ataggtttttatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaatggattatgggcaaatggatttaagagtggttctgcgtgtcaacttccataggtttttatattcaatttacccccctcaaattcttgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCCTGCAACAAGAACGAGCAGCTGGCCGCCAACTACCTCTTGGATCACATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG