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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaaattatgtggttaccaatcaaatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G07770.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G083497_T04 (Zea mays), 5'ss of exon 1
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatg-----attatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaaattatgtggttaccaatcaaatgcag
|||  |||||||||||| |||||  | |||||||||||||||||||||||||| || ||||| ||||| |||||||| ||||  |||||||||   || |||  |     | | ||   ||  |||| |  |   ||  ||||| | ||| |     || |      || |||||  |                  
AAGTCCATGTACAATGCAGAGAAGAGGGGCAAGAGGCAGGTCATGATCAGGCCGTCGTCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGTCATGgttagttctcaatctcgtgccccatttcaattggcagc-attccgaggatacgtacctgattagtgctatattattag------------------

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G177720_T01 (Zea mays), 5'ss of exon 1
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgt--atgattatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaa-attatgtggttaccaatcaaatgcag
|||  ||||||||| ||||||||    |||||||||||||||||||||||||| || ||||| || || |||||||| ||||  |||||||||   ||||||     |  |  | |||  ||    | |   |  || |||    ||||   |    ||| | | |  ||| ||  ||||   |          
AAGTCCATGTACAACGCTGAGAAGATCGGCAAGAGGCAGGTCATGATCAGGCCGTCGTCCAAGGTCATCATCAAGTTCCTGACGGTCATGCAGCGCCACGgttagctagcactcgaccttatgccctgtttcaatgactcc----attccgaggacatgtccatgatcattgtgctgttatgtag---------

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G018228_T04 (Zea mays), 5'ss of exon 2
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaaattat-gtggttaccaatcaaatgcag
|||  ||||||||||||||| ||   ||| ||  | ||||||||||||||||| || ||||| ||||| |||||||| ||||  |||||||||   || |||  |     | || |   || |    | | ||  | | | |     || || | |   ||    |||||  | |||    || |       
AAGTCCATGTACAATGCTGAAAAGATAGGGAAACGTCAGGTCATGATCAGGCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctcctcaacc--ttatgcccatttgaattgcttca----ttctgaggatacgcccctgattattattgttctatattag------

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G328578_T01 (Zea mays), 5'ss of exon 2
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattatcccacca-gattttatata-atagagattcctaagattctcggatgttgttccttaaattatgtggttaccaatcaaatgcag
|||  ||||||||||||||| ||   ||| ||  | ||||||||||||||||| || ||||| ||||| |||||||| ||||  ||||||||     |||  ||| ||| ||| ||   |  ||||    ||    ||| ||    |    ||||     ||| | | |  | | |||    || |       
AAGTCCATGTACAATGCTGAAAAGATAGGGAAACGTCAGGTCATGATCAGGCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCA-----ACGCCATGgttagccctcctcaaccttatgcccatttgaattgcttcattctgaggatacg--tccctgattattattgttctatattag------

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G000801_T01 (Zea mays), 5'ss of exon 1
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaaattatgtggtt-accaatcaaatgcag----------------------------------
         |||||||| |||||  | ||||||||||||||||||||||| || || ||||| ||||| || |||||  |||  |||||||||     ||  |||  ||          ||  ||    | ||   ||  |     | |||| | |  |  |  || |    | |  || || ||||||| |                                  
---------TACAATGCAGAGAAGAGGGGCAAGAGGCAGGTCATGATCAGACCGTCGTCCAAGGTGATCATTAAGTTCATGACGGTCATGCAG-----CGTCATGGATACATTGgtgagttcgattacgtggatgatcacagag--cccggaagcttgtggtggaactgaacgatagactaaacaaatgcggtgtaattagcccctggttcgactttggaataaag

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G018228_T01 (Zea mays), 5'ss of exon 2
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaaattat-gtggttaccaatcaaatgcag
                                       |||||||||||||| || ||||| ||||| |||||||| ||||  |||||||||   || |||  |     | || |   || |    | | ||  | | | |     || || | |   ||    |||||  | |||    || |       
---------------------------------------GTCATGATCAGGCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctcctcaacc--ttatgcccatttgaattgcttca----ttctgaggatacgcccctgattattattgttctatattag------

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|116414319|gb|EG456911.1|EG456911
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|152035691|gb|BP861287.2|BP861287
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|152038400|gb|AV821952.2|AV821952
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|152038534|gb|AV827595.2|AV827595
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|116409593|gb|EG452185.1|EG452185
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|163993997|gb|ES102043.1|ES102043
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTA
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTA
EST: gi|116414320|gb|EG456912.1|EG456912
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|125073205|gb|EL137626.1|EL137626
EST:     TTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: TTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|124711691|gb|EH803093.1|EH803093
EST:     ATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: ATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|152035040|gb|BP842816.2|BP842816
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATGGTCATGCAGAAGCACG                         GTTACATGGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|125116740|gb|EL166160.1|EL166160
EST:     TATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCA
genomic: TATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCA
EST: gi|86081408|gb|DR377165.1|DR377165
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|86075131|gb|DR370888.1|DR370888
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|301502833|gb|HO208373.1|HO208373
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|152035637|gb|BP859475.2|BP859475
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|163971598|gb|ES043350.1|ES043350
EST:     TCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTA
genomic: TCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTA
EST: gi|152037866|gb|BP800725.2|BP800725
EST:     GCCTTC-TCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACGGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
EST: gi|152034265|gb|BP823552.2|BP823552
EST:     GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACG                         GTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG
genomic: GCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattat ... tcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGCATGTACAATGCTGAGAAACGAGGCAAGAGGCAGGTCATGATCAGGCCTTCCTCCAAAGTGATTATCAAGTTTCTGATTGTCATGCAGAAGCACGgtatgattatcccaccagattttatataatagagattcctaagattctcggatgttgttccttaaattatgtggttaccaatcaaatgcag

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