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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattaattattggattggtgataaccacagttgttcacttgcatatttgagtgcataccataaatcaagccttttcttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 9
gtgattaattattggattggtgataaccacagttgttcacttgcatatttgagtg--catacca---taaatcaagccttttcttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG
||||||| ||     |   || | | |  |||  |||    |||| | |||||    |||  ||   |||| || |  |||| ||  | ||||||||||||||||  ||||| || ||| | |||||||||||||| ||||||||||
gtgattatttga-acaccagttacagcagcagccgtttctgtgcacaattgagcagacatgtcaagttaaaccatgttttttttttctacagGCAAGACTTCAGGTGAAGCAAATAATTGATGATGACAAGAGGCACCGCTACAAAG
















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|149071943|gb|EE160330.2|EE160330
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|211285343|gb|FL118292.1|FL118292
EST:     TTGCGAAACTTGGTGCAA-CGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|4681209|gb|AI629879.1|AI629879
EST:     CTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTATCGATGACAAGAGGCATCGCTAC
genomic: CTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|32929166|gb|CF033978.1|CF033978
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|50330442|gb|CO525568.1|CO525568
EST:     AAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: AAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|60343577|gb|DN210550.1|DN210550
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|5714034|gb|AI944019.1|AI944019
EST:     TATCCCCTTTTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCCCATGATTACCGATGCCAAGAGGCATCGCTAC
genomic: TATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|86471991|gb|DY238361.1|DY238361
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|24934302|gb|CA452520.1|CA452520
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|91877626|gb|EB407583.1|EB407583
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|60340184|gb|DN207157.1|DN207157
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|88756339|gb|DY540480.1|DY540480
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|78121536|gb|DV539920.1|DV539920
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|32935002|gb|CF039814.1|CF039814
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|211285345|gb|FL118294.1|FL118294
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|29543455|gb|CB603851.1|CB603851
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|71422917|gb|DR805896.1|DR805896
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGCCAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|32868675|gb|CF008357.1|CF008357
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|211285341|gb|FL118290.1|FL118290
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|211378309|gb|FL452851.1|FL452851
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcacttgcatatttgagtgcataccataaatcaagccttttcttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG
                                       ccttttcttcgtgc  CT-rich tract
                             ataaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattaattattggattggtgataaccacagttgttcacttgcatatttgagtgcataccataaatcaagccttttcttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG