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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagttaatttgctccactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag

Basic information

species Zea mays
transcript GRMZM5G896082_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
---GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagtta-atttgctccac---taactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag
   ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| ||||||||||||||| | |  |  ||  || |  ||  |   || ||  ||| |   |  | |||     |  ||||||  ||||   |      |                                        
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag----------------------------------------

upper sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G14240.1 (Glycine max), 5'ss of exon 3
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgta---agcatttttagttaatttgctccactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag
|| ||||| |||||    ||||| |||||||| || || || || || || |||||||| || ||||||||||| || |||||||| |||||||||||||    |||  ||   |  ||     |  ||     | |    |||  |  || ||      |||   | | |      ||                                           
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatggggcaacttcgctctatagttgcagctgttgtcataacttcatctttttaaagtctttattg--gttgattgtacag-------------------------------------------

upper sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagttaatttgctc-cactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag--
|| ||||| |||||    ||||| |||||||| || || ||||| || || |||||||| || ||||||||||| || |||||||| ||||||||||||| |        |  | ||  ||| || || ||||      |   ||| ||||       |||  || |||| |    |||||    |  ||      || ||   |||  |||| ||  |   
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatga------ggcaacttcactctcagtagctgcagctgttgttgtcattga-------atttgtgttaacgc---gggtgta---tttatcttttttaagtctttgttggttgattgtacag

upper sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagttaatttgctccactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag
 | || || |||||    ||||| || ||||| || ||||| || |||||||||||||| || ||||||||||| || |||||||| || ||||||||||  ||| ||||| | || |    || || ||   || | | ||    ||| || |    ||||     | | | ||  |||    | |    |   |    | | |              
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgta--catatttagattatcttaatcaatatctttatgatat-aatagtttgtaatactttttaa-----atctctaaaatgtaaaattggcttatg-tgtaatgcag--------------

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|149051802|gb|EE155929.2|EE155929
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|149070758|gb|EE159171.2|EE159171
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|71325794|gb|DR799576.1|DR799576
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|76293829|gb|DV033397.1|DV033397
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|50329134|gb|CO524260.1|CO524260
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|148959398|gb|EC905432.2|EC905432
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|78092904|gb|DV521278.1|DV521278
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|71449206|gb|DR830256.1|DR830256
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|74239749|gb|DT647663.1|DT647663
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|71435282|gb|DR816332.1|DR816332
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|50328983|gb|CO524109.1|CO524109
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|71773101|gb|DR971019.1|DR971019
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|93014353|gb|EB639873.1|EB639873
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|149097127|gb|EE182939.2|EE182939
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|37426517|gb|CF651015.1|CF651015
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|33467672|gb|CF244721.1|CF244721
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|211033504|gb|FL333366.1|FL333366
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|149111107|gb|EE294603.2|EE294603
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|149058763|gb|EE156781.2|EE156781
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|71322554|gb|DR797954.1|DR797954
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|148971891|gb|EE022659.2|EE022659
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|78114034|gb|DV532423.1|DV532423
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|71775245|gb|DR973123.1|DR973123
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|89757906|gb|DY687292.1|DY687292
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|211111363|gb|FL325867.1|FL325867
EST:     AACCTCAAGGAGGAGCTCATGTGGGAANGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: AACCTCAAGGAGGAGCTCATGTGGGAG-GGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|149011246|gb|EE042332.2|EE042332
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|78107802|gb|DV526220.1|DV526220
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
EST: gi|148949267|gb|EC894710.2|EC894710
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA                         ACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcattt ... ttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagttaatttgctccactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG