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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaagttggtgtttttttactctctgtttcacaagagtttcatttcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA

Basic information

species Arabidopsis thaliana
transcript AT2G37600.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 2
gttaagttggtgtttttttact-ctctgtttcacaagagtttcatttcactgactttggtaattcatt----tctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
      |   || |||  | || || | | | |   |  || || || |||| |  |  |     |||    |  ||      |||||   || ||  | |  ||||| | | |||||||   |  ||  | || ||  |||| ||||| || |||||| | ||||| ||||||||| | ||||||||||||||||| ||||| |
-----ttcaatgatttgatcctgctttatattatctgctttgcagtttactggccattatttcctattgcatttgcacttaccttgttggcatgttaatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCTGGATTTGCTCCCTATGAGAAGCGTATCACTGAGCTTCTCAAAGTTGGCA

upper sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g62350.1 (Oryza sativa), 3'ss of exon 2
gttaagttggtgtttttttactctctgtttcacaagagttt-catttcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
    || |    |||  |  ||  ||| |  | | |    | ||    |    |||      |  |||  |  |    | ||||||  | | ||  |  ||||||  | ||||||    |  ||  | ||     |||||||||| || |  ||| | ||||| ||||||||  |||||||||||||||| |||||||| |
-cagagatttcttttgctgtcttcctgatgaatacggccatacaccatagctgcttcctatttatattctttcattaatatgttttcttgtcttattgcagAAAAGTACCAAGAGAGTGAATTTTGTCAGGGGCTTGATTAGGGAGGTTGTGGGATTTGCTCCATATGAGAAACGAATCACTGAGCTTCTGAAGGTTGGAA

upper sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G850966_T03 (Zea mays), 3'ss of exon 2
gttaagttggtgtttttttactctctgt-ttcacaagagtttcatttcactg-actttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
  |      ||   |  |||      || | |   ||| || ||| ||  || ||||   |  ||  | | ||     ||     || || || ||||| ||||| | |  ||||||       |  | ||    ||||| || || || |||||  | ||||||||||||||| | |||||||||||||| |||||||| |
-ctgtacatgtaaatgattagcacaagtatgcggtagatttacatatctttgcacttgattgttttctgtgtccttcattccaagtt-attttgttgttcagAAATCAACGAAGAGGGTGTCTATGGTCAGGGGCCTGATCAGAGAGGTTGCTGGGTTTGCTCCTTATGAGAAGCGTATCACTGAGCTTCTGAAGGTTGGCA

upper sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G850966_T01 (Zea mays), 3'ss of exon 3
gttaagttggtgtttttttactctctgtttcacaagagtttcatttcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
      |  | |   ||      | || | |  | |||   | | |||||||  ||   ||           | |    ||   |||   ||  | | ||| || |      |    ||       ||  ||   ||    |||  | || ||                                               
-cctgatcagagaggttgctgggtttgctccttatgagaagcgtatcactgAGCTTCTGAAGGTTGGCAAGGACAAGCGTGCCCTGAAGCTT--GCTAAGAGAAAGCTTGGAACTCACAAGAGGGCAAAGAAGAAGAGAGAGGAGATGGCGGG-----------------------------------------------

upper sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009936_T01 (Zea mays), 3'ss of exon 2
gttaagttggtgtttttttactctctgtttcacaagagtttcatttcactgactttggtaattcatt-tctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
     ||   ||  |  |     |||| |  ||  |  | |  |||   |    ||| | |||   | |  |     || |   || ||  | |  || ||||| | |  ||||||       |  | ||    ||||| || || || |||||  | ||||||||||||||| | ||||| |||||||| |||||||| |
cacttgtaaatggctcatataaatctggtggacttgcatatgtttttttttcacttgatgattttctgtgccctttattgtaacttcatggtgt-attcagAAAGCAACGAAGAGGGTGTCCATGGTCAGGGGCCTGATCAGAGAGGTTGCTGGCTTTGCTCCTTATGAGAAGCGTATCACCGAGCTTCTGAAGGTTGGCA

upper sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
---gttaagttggtgtttttttactctctgtttcacaagagtttcatttcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
   ||||| ||   ||||||||  |   | |||   |||| | | || |     |   ||  | |   ||  |           |||||    | |  || ||||||| |||||||||  |   ||| |||| ||  |||| |||||||| |||||  | || || ||||||||||||||||||||||||||||| |||||||
atggttaaattacagttttttt-ttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttggg--tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA

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|86079643|gb|DR375400.1|DR375400
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024752|gb|DR320505.1|DR320505
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024747|gb|DR320500.1|DR320500
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86035294|gb|DR331047.1|DR331047
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAMAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024757|gb|DR320510.1|DR320510
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024754|gb|DR320507.1|DR320507
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024749|gb|DR320502.1|DR320502
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024744|gb|DR320497.1|DR320497
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024742|gb|DR320495.1|DR320495
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024750|gb|DR320503.1|DR320503
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024740|gb|DR320493.1|DR320493
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024741|gb|DR320494.1|DR320494
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|125197184|gb|EL212138.1|EL212138
EST:     ACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024753|gb|DR320506.1|DR320506
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024748|gb|DR320501.1|DR320501
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86035293|gb|DR331046.1|DR331046
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024755|gb|DR320508.1|DR320508
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024751|gb|DR320504.1|DR320504
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024739|gb|DR320492.1|DR320492
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024756|gb|DR320509.1|DR320509
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024746|gb|DR320499.1|DR320499
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024759|gb|DR320512.1|DR320512
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
EST: gi|86024745|gb|DR320498.1|DR320498
EST:     ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGG                         AAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT
genomic: ACGTCGTCACCAGACGTGAGCTAGCTCCTCGTCCCAATTCTCGCAAAGGGgtatcaatct ... ttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA
                                            tttttgttt  CT-rich tract
                               ttttgttttgatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagttggtgtttttttactctctgtttcacaagagtttcatttcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT