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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactcccatcatctgtttttaagctttcttttagttataaatttggtattgatgatcagatatgccactgtttccattacag

Basic information

species Zea mays
transcript GRMZM2G153393_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgta------cactcccatcatctgt------ttttaagctttcttttagttataaatttggt----attgatgatca--gatatgccactgt----ttccattacag
|||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||||| |||||||| || || ||||| ||||| ||||| || || |||||         || |||||   ||      |||  ||||| |   ||  ||||||||| ||    | |||||| |   | |||     |||    || ||||||||
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaacttgatcttctcatcagtcgtaaccagtttccagcttgcgcataactataaatttagtgctaactgatgaacctcggtataatcgtgtgactttgcattacag

upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G42360.1 (Glycine max), 5'ss of exon 16
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactcccatcatctgtttt--taagctttc----ttttagttataaatttg---gtattgatgat---cagatatgccactgtttcc-----attacag---------------
| ||||| | | || | |||||||| ||  | || |||||||||||||||||||||||||||||| | |||||  | |  ||||| | ||||||||| ||||  | |       | | ||||  |  ||| ||    ||||    |  | | ||     |||||   |    ||||||   | ||||  |     ||| |                 
CTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTTGTCATGTTGGAACTTCTCAGCGGACGGAAACCATTTGATAGgtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaattgaaattatgtagatataataatgttgtctcctgattgcgaaacattctgtaacag

upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G45130.1 (Glycine max), 5'ss of exon 14
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacact---------cccatcatctgtttttaagctttcttttagt----tataaatttggtattgatgatcagata-tgccactgtttcc--attacag---------------
| ||||| | | || | |||||||| ||  | || ||||||||||||||||||||||| |||||| | |||||  | |  ||||| |  || ||||| ||||  | |         |      |||| | | | | |||     | |    |  | |||| | | | |||  || ||| |     ||| |||  ||| ||                
CTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTCGTCATGTTGGAACTTCTCAGTGGACGGAACCCTTTTGATAGgtgaattaatggttttctttatgtctgctctcacgtttttgagcaatattctgcagattttgaaattatgcacaaataataatgttgtctcctgattgcaaaacattccatgacag

upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactcccatcatctgtttttaagctttcttttagttataaatttg-gtattgatgatcagatatgccactgtttccattacag------------------------
| ||||| | | || | ||||| || || || ||||||||||| || |||||||||||||||||| | |||||  | |  ||||| | ||||||||| ||||  |      | || |   ||||||     |   |||| ||  |||   | |  |   |   | |    | ||    |||  | |                        
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagat--tgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaacgttccttcttcag

upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S279_14V6.1 (Physcomitrella patens), 5'ss of exon 4
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGg---tacactcccatcatctgtttttaagctttcttttagttataaatt-tggtattgatgatcagatatgccactgtttccattacag--------------------
          |||| | ||    |||    | ||| ||||||| ||||||||||||||||||||| | || ||  | || || || |  ||  | ||||||    ||   ||  |  | ||       | |     ||  ||| ||  |   |||||  |  ||   |       || || |     ||                    
---------CCATGTCTGGAACATACGATGTGAAGGGTGATGTTTACAGCTTTGGAGTTGTCATGTTCGAGCTCATTACTGGGCGCAAGCCTCTGGACAGGGGACACGAgccttttgtttgaagaggggttcatcatttcttagaatctgctgtatttgtactcgtttcatttgatgcttgctggtaagtgcatgagacgcgcatagcc

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|211336842|gb|FL296073.1|FL296073
EST:     ACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: ACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|40303178|gb|CK347565.1|CK347565
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|149106214|gb|EE291907.2|EE291907
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|40303248|gb|CK347635.1|CK347635
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTTGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|18177140|gb|BM378350.1|BM378350
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|32845826|gb|CD985507.1|CD985507
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|101388907|gb|EB816435.1|EB816435
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|211334695|gb|FL296071.1|FL296071
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|67014194|gb|CO442943.1|CO442943
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|211334696|gb|FL296072.1|FL296072
EST:     TTTGGAGTTGTMATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|71442374|gb|DR823424.1|DR823424
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|60395662|gb|DN228532.1|DN228532
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|32838090|gb|CD977768.1|CD977768
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCTGGTGGGCAACACCCCAGC
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGC-GGTGGGCAACACCCCAGC
EST: gi|32847053|gb|CD986734.1|CD986734
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|213182930|gb|FM185306.1|FM185306
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|211334693|gb|FL296069.1|FL296069
EST:     TTGGAGTTGTCATGCTTGAACTATTGATAGGACGTATGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTGGAGTTGTCATGCTTGAACTATTGACAGGACGTA-GACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|32848553|gb|CD988234.1|CD988234
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|101390185|gb|EB817025.1|EB817025
EST:     TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAG                         CTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: TTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT
EST: gi|32847233|gb|CD986914.1|CD986914
EST:     CATGCTTGAACTATTGACAGGACGTAGCCCATTTGACAG                         CTCTAGACCCAGGTCAGAACAGTCACTTGTGCGGTGGGCAACACCCCAGCT
genomic: CATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactccc ... tccattacagCTCTAGACCCAGGTCAGAGCAGTCACTTGTGCGGTGGGCAACACCCCAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactcccatcatctgtttttaagctttcttttagttataaatttggtattgatgatcagatatgccactgtttccattacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG