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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCATCGACATCGTCGAGCTCTGCTACAAGGCCGGCGCGTGGAAGACGCTAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttctcgagaattcaccgccttgctcttacatccccgttttttttttttggtgtaatcagtatatgtgtatgagaccctttagaggtactttagt...

Basic information

species Zea mays
transcript GRMZM2G013750_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 2
CGTCATCGACATCGTCGAGCTCTGCTACAAGGCCGGCGCGTGGAAGACGCTAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttctcgagaattcaccgccttgctcttacatccccgttttttttttttggtgtaatcagtatatgtgtatgagaccctttagaggtactttagt--------
|| |||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||  |||||||||||||||| |||||||||||||||||   | |||||     ||  | |||   ||||    |  |||||  |  || | ||  ||| | ||  ||| | | ||     | |  | ||  ||           
CGCCATCGACATCGTCGAGCTCTGCTACAAGGCCGGCGCCTGGAAGACGCTCAACGATCAGATCGTGGTCCTCTCCAAGAGGAGGGGCCAGCTTAAGCAGgtcaagctctcg-----tcctctccta--tctttggacttcgtttagtagttctagttgaattactagctgtattt-agctatctaactgatatcttcaaagttatac
















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:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|33095283|gb|CF055277.1|CF055277
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAGTGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|13557648|gb|BG549004.1|BG549004
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|60341151|gb|DN208124.1|DN208124
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|67017748|gb|CO446497.1|CO446497
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211430132|gb|FL338157.1|FL338157
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211053473|gb|FL477603.1|FL477603
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|149074396|gb|EE162784.2|EE162784
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|18169982|gb|BM339822.1|BM339822
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGATTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|31909275|gb|CD650837.1|CD650837
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|32847815|gb|CD987496.1|CD987496
EST:     TAAACGACCAGACCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGTCTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|120480672|gb|EH210948.1|EH210948
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|40337465|gb|CK371535.1|CK371535
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|149084023|gb|EE173418.2|EE173418
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|149078169|gb|EE166920.2|EE166920
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211157243|gb|FL334276.1|FL334276
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|18175563|gb|BM350832.1|BM350832
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|4753426|gb|AI657336.1|AI657336
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|17930979|gb|BM267939.1|BM267939
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|18166766|gb|BM336605.1|BM336605
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAACAATGGAATACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|148945292|gb|EC890506.2|EC890506
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211187929|gb|FL314081.1|FL314081
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGAT
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGAT
EST: gi|148945727|gb|EC891006.2|EC891006
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211535625|gb|FL478806.1|FL478806
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|20803197|gb|BQ294247.1|BQ294247
EST:     AAACGACCTGTATCGGTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGGTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: AAACGACCAG-ATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|67013990|gb|CO442739.1|CO442739
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|60358562|gb|DN225535.1|DN225535
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|9952312|gb|BE638895.1|BE638895
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211040418|gb|FL321548.1|FL321548
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCATCGACATCGTCGAGCTCTGCTACAAGGCCGGCGCGTGGAAGACGCTAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttctcgagaattcaccgccttgctcttacatccccgttttttttttttggtgtaatcagtatatgtgtatgagaccctttagaggtactttagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catccccg