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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAATGTGTTCTTGAGGATAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcatttttgtgcctgttttgttttttttcctgcatgagcgtcatttaaaaaaggtgtgttttttgacaatgtatatcatatctagctttctctcga...

Basic information

species Zea mays
transcript GRMZM5G859195_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G859195_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g58790.2 (Oryza sativa), 5'ss of exon 3
ATTAATGTGTTCTTGAGGATAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcatttt---tgtgcctgttttgttttttttcctgcatgagcgtcatttaaaaaaggtgtgttttttgacaatgtatatcatatctagctttctctcga----------
|||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||   ||| |||| |||| | | |  | ||||||| |||      | |||||||| ||     ||| |  |||  ||||| |  ||| ||              
ATTAATGTGTTCTTGAGGATAACGGGTAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTGTTTCATgtgagcattttacttgtacctgctttgatatgt--catgcatgaacgt------acaaaggtgtttt-----acagttcataatatatccatttttttcaatgttcaaaaata
















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|211042886|gb|FL185936.1|FL185936
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAA
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAA
EST: gi|71768978|gb|DR966915.1|DR966915
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|116821910|gb|EC865263.1|EC865263
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTAGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|211042883|gb|FL185933.1|FL185933
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|148969055|gb|EE019774.2|EE019774
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|148955559|gb|EC901197.2|EC901197
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|76021627|gb|DT948797.1|DT948797
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|91870954|gb|EB401166.1|EB401166
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|211042884|gb|FL185934.1|FL185934
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTYAT                         GTCATAAGTTTGGGTGATACTATCAWATTCTCATTGTTCACCAAGTAAAAG
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGT-CACCAAGTAAAAG
EST: gi|211042881|gb|FL185931.1|FL185931
EST:     TAACGGGCWAGAGACCAGATGGGTTCCATGACCTGGCNTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATC
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATC
EST: gi|13558408|gb|BG549764.1|BG549764
EST:     TAACGGGCAAGAGACCAGATGGGCTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGT
EST: gi|149080472|gb|EE169502.2|EE169502
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|211042885|gb|FL185935.1|FL185935
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTA
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTA
EST: gi|13198608|gb|BG354410.1|BG354410
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAAATTCTCATTGTCACCAAGTAAAAGT
EST: gi|211042888|gb|FL185938.1|FL185938
EST:     TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCAT                         GTCATAAGTTTGGGTGATACTATCAA
genomic: TAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcattt ... aactttccagGTCATAAGTTTGGGTGATACTATCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAATGTGTTCTTGAGGATAACGGGCAAGAGACCAGATGGGTTCCATGACCTGGCTTCTCTATTTCATgtgagcatttttgtgcctgttttgttttttttcctgcatgagcgtcatttaaaaaaggtgtgttttttgacaatgtatatcatatctagctttctctcga

- - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaag