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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacag

Basic information

species Zea mays
transcript GRMZM2G013750_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 5
GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacag
|| |||||||||||||||||||||||||| || || ||||| |||||||| |||||||||   ||   |  ||   |  |||  |||   ||| |||| ||||| ||   |  ||  || |||||| | ||  |  ||||||
GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgta---tgaagaaatacagtaataaagcttgaaattgttac-aaaagcctgggttctg-gaatcttactgtaatcatgatcacag

upper sequence: GRMZM2G013750_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 5
GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgta--acgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacag----------------------
|| |||||||| ||  ||||||| ||||| ||||||||||| ||||||||||| || |||  |  |       | |||   | ||     | | |   | |  |    ||  |  ||    | || |  ||  || | ||| |                       
GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAAgtatgagatatttttgtgttactgtgatgaca-gcaatagcaggtcactaatttcttgtgttgcaatt-cagttgctgatatcagaatcttccatgtcaaattgtatag

upper sequence: GRMZM2G013750_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 5'ss of exon 5
GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacg-----tgccaacctattatgttaat---actttgtatttttacgaaaaggcttattc--atgcaaaacttactattattgttgtcacag---------
|| || ||||||||  | |||||||| || ||||||||||||||||||||||| || ||||       ||  | | | | || ||  |    ||||||  |||          ||| ||   |||      ||   ||||||| |||   |          
GTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAAgtaagactttctgttatcttttcatatttcttaagctttgtgctttgtgctttgttcttgtttgtatgttgtgattctaattattggtgtgtaaacttctgaag

upper sequence: GRMZM2G013750_T04 (Zea mays), 5'ss of exon 5
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 5
GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttat---tcatgcaaaacttactattattgttgtcacag-------------------------------
|| || || || ||  | ||||||||||| |||||||||||||||||||| |||||||||| |      | |    |     ||   ||||| |    |       |||      || |  ||  |   | | | ||  |  | |                               
GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAGgtaaggaaatttcttggctttacgctatgctgtatatgctagctcgtatttaggaacgatactgaagctttcagtttggtactttccgaatcattactcatattagaatgatgttgcag

upper sequence: GRMZM2G013750_T04 (Zea mays), 5'ss of exon 5
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 5'ss of exon 5
GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacg-------------tgccaacctattatgttaa-tactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacag----------------------------------------------------
|| ||||| |||||  |||||||||| || ||||| ||||||||||||||||| || |||| |             ||| | ||| || |   |  |||||||  |||     |||  |  | |  ||  ||    |     |     | ||  ||                                                    
GTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAAgtaaggatttttttatatttgcaatcctgttttaccagctactttgcgtttggtttaaatagtatttgtattgaagttcttgagctggcact-tcgaagttcttaccgttattttgttagagccagtactgatagtagggtggtgtgccag

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|60352441|gb|DN219414.1|DN219414
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|33095283|gb|CF055277.1|CF055277
EST:     CATTTGGCTCCATGGCAAAGACGGAAAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|60341151|gb|DN208124.1|DN208124
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCTGCTATGCCTAAATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGA
EST: gi|67017748|gb|CO446497.1|CO446497
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|211430132|gb|FL338157.1|FL338157
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|211053473|gb|FL477603.1|FL477603
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|149074396|gb|EE162784.2|EE162784
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|18169982|gb|BM339822.1|BM339822
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|166663766|gb|EG139356.1|EG139356
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTA
EST: gi|32847815|gb|CD987496.1|CD987496
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|5847143|gb|AW000222.1|AW000222
EST:     AAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCA
genomic: AAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|120480672|gb|EH210948.1|EH210948
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTAT
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTAT
EST: gi|40337465|gb|CK371535.1|CK371535
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|149084023|gb|EE173418.2|EE173418
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|149078169|gb|EE166920.2|EE166920
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGA
EST: gi|18175563|gb|BM350832.1|BM350832
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|17930979|gb|BM267939.1|BM267939
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|32824870|gb|CD964592.1|CD964592
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|60349290|gb|DN216263.1|DN216263
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|18166766|gb|BM336605.1|BM336605
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCGCAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|148945292|gb|EC890506.2|EC890506
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGT
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGT
EST: gi|148945727|gb|EC891006.2|EC891006
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|211535625|gb|FL478806.1|FL478806
EST:     CATTTGCCTCCATGGCAAAGACGGAGAAAATTCCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATCATGTTCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|211088675|gb|FL328946.1|FL328946
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     CATTTGGCTCCCTGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGAT
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGAT
EST: gi|67013990|gb|CO442739.1|CO442739
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA
EST: gi|60358562|gb|DN225535.1|DN225535
EST:     CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCA
EST: gi|211040418|gb|FL321548.1|FL321548
EST:     CATTTTGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTAGATCGTCAAGATTATGTTCGAGCACNAATTTTATCA
genomic: CATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgcc ... gttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacag

- - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG