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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCGCATAGCGCCAGGCGTGGGCGCGAACCTACTCGGGCAGCACTCAGCGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttcccacataccctcgctattgcgattcctaggtccccgccgatgataaagttatccctaaagcacataattacttgtgtgaactggtgaccc...

Basic information

species Zea mays
transcript GRMZM2G102639_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102639_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 5'ss of exon 1
GACCCGCATAGCGCCAGGCGTGGGCGCGAACCTACTCGGGCAGCACTCAGCGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttcccacataccctcgctattgcgattcctaggtccccgccgatgataaagttatccctaaagc------acataattacttgtgtgaactggtgaccc
||| ||||| ||||| ||||||||||| ||||| |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||  |     || |||  | | ||      ||| |||  | || || |  | | ||| ||||      |   |    |||||  |  |   || | |
GACGCGCATCGCGCCCGGCGTGGGCGCCAACCTGCTCGGGCAGCACTCGGCGGAGCGGAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCCCAGgttagggttcctcccccttcttgctcctcccatct----gtcgccgtagctg-tagatgtgttcctgaagcctccacagggaggggcttgta-gcgcccatggctc

upper sequence: GRMZM2G102639_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S70_254V6.1 (Physcomitrella patens), 5'ss of exon 1
GACCCGCATAGCGCCAGGCGTGGGCGCGAACCTACTCGGGCAGCACTCAGCGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgt-----tagggttcccacataccctcgctat-----tgcgattcctaggtccccgccgatgataaagttatccctaaagcacataattacttgtgtgaactggtgaccc
||| |||||  |||| || ||||| || ||||| || || || ||| | || ||||| |||||||| || ||| | |||||||||||||||||| |||||||     |  ||||  | | |   ||||  ||     | | | |   ||    |   |     |  |     |  |   |   |||   ||| |  |  | | |      
GACGCGCATCACGCCCGGTGTGGGTGCCAACCTCCTTGGCCAACACGCCGCTGAGCGTAACCAGGATGCGACCGCTTACGTCGGCAACCTCGACTCTCAGgtgtctgtctggtttgcgcctcttctcgtcatgaatttactactatcagtcttctttctcctgtggaacccgcttttggga--atagccactcggct--attag------
















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|26558877|gb|CA831112.1|CA831112
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|78090866|gb|DV519240.1|DV519240
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|91056510|gb|EB166928.1|EB166928
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|148943004|gb|EC888052.2|EC888052
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|87157489|gb|DY402278.1|DY402278
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|33467168|gb|CF244217.1|CF244217
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|148956981|gb|EC902927.2|EC902927
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|148933043|gb|EE285938.2|EE285938
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|78124664|gb|DV543048.1|DV543048
EST:     CGGAGCGCAACCAGGACGCCCCCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGAAATTGTTTGTCCAAGCGGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|50322326|gb|CO517452.1|CO517452
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|89762379|gb|DY689990.1|DY689990
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|94477767|gb|EB706725.1|EB706725
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|76288123|gb|DV027691.1|DV027691
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|71425499|gb|DR806709.1|DR806709
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|76291455|gb|DV031023.1|DV031023
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|76015742|gb|DT942912.1|DT942912
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|76290093|gb|DV029661.1|DV029661
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|148961210|gb|EE011925.2|EE011925
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCC-TGTTG
EST: gi|86472905|gb|DY239275.1|DY239275
EST:     CGGAGCGCACCCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGAAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|78124734|gb|DV543118.1|DV543118
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGAAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGAAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
EST: gi|148938096|gb|EC882358.2|EC882358
EST:     CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAG                         GTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG
genomic: CGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttc ... tatatgacagGTTTCTGAGGAGCTTCTATGGGAATTGTTTGTCCAAGCAGGCCCTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCGCATAGCGCCAGGCGTGGGCGCGAACCTACTCGGGCAGCACTCAGCGGAGCGCAACCAGGACGCCACCACCTACGTCGGCAACCTCGACCCTCAGgttagggttcccacataccctcgctattgcgattcctaggtccccgccgatgataaagttatccctaaagcacataattacttgtgtgaactggtgaccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccgcc