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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGTGGCCTTCACCTACGACGGCGTCCCTCTTCTTGCGATGCTGGACGAATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcagtgttcacggctgctgcttcctgtgactggttcatgagccacactgtctaatcacctcgttgcctttcag

Basic information

species Zea mays
transcript GRMZM2G112337_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 5'ss of exon 9
TGGCGTGGCCTTCACCTACGACGGCGTCCCTCTTCTTGCGATGCTGGACGAATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgta---ttctcagtgttcacggctgctgcttcctgtgactggttcatgagccacactgtctaatcacctcgttgcctttcag------------
|||  || | |||| ||| ||||| || | |||||| || |||||||| || |||||| | || |||||| |||||||||| |||||||||||||||||||||   ||||      || |   |  |  |||   || |||| ||   | ||| |      | ||   | | |  ||| ||             
TGGTATGCCGTTCAGCTATGACGGTGTTCATCTTCTCGCAATGCTGGATGAGTACAAAGTACTAAGGCAGCAGAAGGAAGAAGAGAAGCGACGAATGAGGgtacccttctgtccaatccccattaatctttcgcatgtctggctctaaaaccatatc--tcattccatttgctttcttccaaaactcatttcag
















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|87157169|gb|DY401958.1|DY401958
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|88756750|gb|DY540891.1|DY540891
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|148995697|gb|EE034920.2|EE034920
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|71771989|gb|DR969926.1|DR969926
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|67021761|gb|CO450510.1|CO450510
EST:     AATACAAAATCCTGAGGCANGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCANNNAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|71773221|gb|DR971130.1|DR971130
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|148928684|gb|EC873287.2|EC873287
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|89249959|gb|DY621745.1|DY621745
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|211026266|gb|FL455139.1|FL455139
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCSACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|71306089|gb|DR789194.1|DR789194
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|15426945|gb|BI542767.1|BI542767
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCCCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|71435944|gb|DR816994.1|DR816994
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|149098529|gb|EE184515.2|EE184515
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|22820000|gb|BU500090.1|BU500090
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|60351440|gb|DN218413.1|DN218413
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|149078381|gb|EE167156.2|EE167156
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|89763677|gb|DY690772.1|DY690772
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|67020793|gb|CO449542.1|CO449542
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|211163232|gb|FL071797.1|FL071797
EST:     GGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: GGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|149088740|gb|EE177864.2|EE177864
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|15352994|gb|BI502605.1|BI502605
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
EST: gi|211373071|gb|FL457566.1|FL457566
EST:     AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGG                         GACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC
genomic: AATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcag ... tgcctttcagGACCAGAAAAAGATGAACGAACAGCTAGCCGCCGAACAGGAGAAGCTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGTGGCCTTCACCTACGACGGCGTCCCTCTTCTTGCGATGCTGGACGAATACAAAATCCTGAGGCAGGAGAAGGAAGACGAGAAGCGACGAATGAGGgtattctcagtgttcacggctgctgcttcctgtgactggttcatgagccacactgtctaatcacctcgttgcctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC