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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaaatgaaataaataaacctatgcttatttatttatagaactgcacatttatctggctcattaatttccccacttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGGTGTGGACCCTGTTTGGCATGGTAGCCGCAGCGAGCTGCCGTTTCTCAAT

Basic information

species Zea mays
transcript GRMZM2G104418_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 12
gtaaggaaaatgaaataaataaacctatgcttatttatttatagaactgcacatttat-ctggctcattaatttccccacttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGGTGTGGACCCTGTTTGGCATGGTAGCCGCAGCGAGCTGCCGTTTCTCAAT
||||| |||| |    ||| ||| | | | || | |   | || ||  | | |||||| |   || |||  ||  |       ||  ||| |||||| | || |||||| || | |||||||||    ||||||||||||||||||||||||| |||||||| |||||||||||| ||||||||||||| 
gtaagaaaaa-gtttcaaacaaaaccacgtttttatccctttaaaaaagaatatttatgcctacttattgtttgtcttgtggatt--tagAGATGCTGCAACAGAAGGATTACTCAAGGTAAGACGGACATACCCTTTTGGTGTGGACCCTGTATGGCATGGCAGCCGCAGCGAGTTGCCGTTTCTCAAC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaggaaaatgaaat--aaataaacctatgcttatttatttatagaac-tgcacatttatctggctcattaatttccccacttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGGTGTGGACCCTGTTTGGCATGGTAGCCGCAGCGAGCTGCCGTTTCTCAAT
||| |  || |       |||      ||     ||  ||| |  |||  |    |    ||||  |   |   |||  | ||  |    ||||| ||||||||    || || || ||     ||||  | || || ||||||||||| ||||| |||||||||| |||||| ||||| || || || |||
gtatgtcaacttgttctcaaacccctttaaaggaatgcattaaaggaatatctttaagattctgagtttctgtcttctgctctcttgttcagTGAGGCTACTACAATTGGTCTGATCAAAACCCGAGACACTTATCCATTTGGTGTGGATCCTGTGTGGCATGGTACCCGCAGTGAGCTACCATTCCTAAAT

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 12
----gtaaggaaaatgaaataa-ataaacctatgcttatttat---ttatagaactgcacatttatctggctcattaatttccccacttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGGTGTGGACCCTGTTTGGCATGGTAGCCGCAGCGAGCTGCCGTTTCTCAAT
     | |  |||    | | | || |   |    || |||     ||||| |    |  |  |  |   || | || | | |  |||  ||   || |||||| | || |  ||  ||||||||||  |     | ||||| ||||||||||||||||| |||||||||  ||||||||| ||||| || ||||| 
gtatttgacaaaaccctagttacatcatattggatttttttgcctattatacattctcttaaattccattcttagtattcttcatactcttttgcagGGATGCTTCAACAGCGGGCTTAATTAAGGTGCGTCGCACTTACCCATTTGGTGTGGACCCTGTATGGCATGGTTCCCGCAGCGAACTGCCATTCCTCAAC

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|32929086|gb|CF033898.1|CF033898
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|94475016|gb|EB703974.1|EB703974
EST:     TGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|32929323|gb|CF034135.1|CF034135
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|211366580|gb|FK956889.1|FK956889
EST:     GTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: GTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|32929184|gb|CF033996.1|CF033996
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|32930632|gb|CF035444.1|CF035444
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|78080517|gb|DV508929.1|DV508929
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|32929163|gb|CF033975.1|CF033975
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
EST: gi|32928488|gb|CF033300.1|CF033300
EST:     TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAG                         TGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG
genomic: TTTGGGCTTTTTGGTAAATCTGCCTATGCATGCCGTGATTCTTCTTGTAGgtaaggaaaa ... ttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttatagaactgcacatttatctggctcattaatttccccacttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGGTGTGGACCCTGTTTGGCATGGTAGCCGCAGCGAGCTGCCGTTTCTCAAT
                              cattaat  putative branch site (score: 3)
                                    tttccccacttgttc  CT-rich tract
                             tcattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaaaatgaaataaataaacctatgcttatttatttatagaactgcacatttatctggctcattaatttccccacttgttcatagTGATGCTACTACTGAAGGACTAATTAAGGTAAGAGATGCATACCCTTTTGGTGTGGACCCTGTTTGGCATGGTAGCCGCAGCGAGCTGCCGTTTCTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC