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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgctgttgttccttgcccctgctacctttgtatctaatattctaatgtaaaaataaatgatagtattgtccttgtcttgggggggatgcaagt...

Basic information

species Zea mays
transcript GRMZM2G060977_T05
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060977_T05 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 12
CAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgctgttgt-tccttgcccctgctacctttgtatctaatattctaatgtaaaaataaatgatagtattgtccttgtcttgggggggatgcaagt---------------------
 |||||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||||||| || ||| |||||| | ||||| ||  ||  || ||      | ||  ||  | ||   |||  ||    | |      |    |  | | |                     
TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtgacaatgtcaaccttagcttttctttggggaaaagaaaaacactaatcataccattccaatgtttcag
















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|211495481|gb|FL464081.1|FL464081
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|78107953|gb|DV526371.1|DV526371
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTTTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|60352542|gb|DN219515.1|DN219515
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|148949106|gb|EC894535.2|EC894535
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|6538840|gb|AW224979.1|AW224979
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACCCAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|149085023|gb|EE174532.2|EE174532
EST:     GTGTGGCAGAACGAGTAGTTCGTAGAAGCCATGAAATTTTAGGCCATGAG                         GTTGCAATAGACACAGCGGCCCCCCTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|113702665|gb|EE680169.1|EE680169
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|9730867|gb|BE509619.1|BE509619
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|37395454|gb|CF635007.1|CF635007
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|60342148|gb|DN209121.1|DN209121
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|60342166|gb|DN209139.1|DN209139
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|88746930|gb|DY531071.1|DY531071
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTTTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|148942651|gb|EC887670.2|EC887670
EST:     GTGTGGCAGAACGAGTAGTTCGTAGAAGCCATGAAATTTTAGGCCATGGG                         GTTGCAATAGACACAGCGGCCCCCCTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|60397921|gb|DN230737.1|DN230737
EST:     AACGAGTAGCTCGTAGAAGCCCTGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: AACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|211424816|gb|FL445164.1|FL445164
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|211138006|gb|FL213711.1|FL213711
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|37397094|gb|CF635842.1|CF635842
EST:     GTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|32864876|gb|CF004558.1|CF004558
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
EST: gi|40336792|gb|CK370862.1|CK370862
EST:     GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAG                         GTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG
genomic: GTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgc ... tttctttcagGTTGCAATAGACACAGCGGCACCACTTGAGAATGATTCAGCTGCTGGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgctgttgttccttgcccctgctacctttgtatctaatattctaatgtaaaaataaatgatagtattgtccttgtcttgggggggatgcaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC