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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTGCCAAGAAACAGAGACTTCTCTGGGCATCAACAAGTGTAAAGAACCCAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatctttttgtttgtgttgaagtcaataggctgtattaacgctttggaagtatattcatagtttttgtgggtgtgatttag

Basic information

species Arabidopsis thaliana
transcript AT5G13420.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13420.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G47790.3 (Glycine max), 5'ss of exon 5
AGGTGCCAAGAAACAGAGACTTCTCTGGGCATCAACAAGTGTAAAGAACCCAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatctttttgtttgtgttgaagtcaataggctgtattaacgctttggaagtatattcatagtttttgtgggtgtgatttag----------------------------------------------------------------------------------------------------
 || |||||||| || || || || ||||| ||||| |||||||||||||| || || ||||||||||||||||| |||||||| || ||||| ||||||||||| |||| |||| |||   ||   | ||||    | || | | | |   |  |       | |  | ||  || |  | ||||                                                                                                     
GGGGGCCAAGAAGCAAAGGCTCCTTTGGGCCTCAACCAGTGTAAAGAACCCTGCCTATTCTGACACCTTATATGTTGCTCCTCTTATTGGACCCGACACTgtaagccatcattttttttcacttt--gccaattttttataattatgttcgagttgatctaaaacaaatatta-ggattagctttaaaggacttgtttgttgtctggccttgtttgtgttaaagaaacttaaaaaccatagtttcctttgctgtatctcatcatagcaataccttgttactttccag

upper sequence: AT5G13420.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G53700.1 (Glycine max), 5'ss of exon 6
-AGGTGCCAAGAAACAGAGACTTCTCTGGGCATCAACAAGTGTAAAGAACCCAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatctttttgtttgtgttg--aagtcaataggctgtattaacgctttgg-----aagt--atattcatagtttttgtgggtgtgatt-tag----------------------------------------------------------------------------------
  || |||||||| || || || |||||||| ||||| ||||||||||| || || || ||||||||||||||||| |||||||| || ||||| ||||||||||| |||| |||| ||    ||   || |   |      ||| | ||  |||      |||   |||||  ||| |||  |||   || || | |                                                                                  
AGGGGGCCAAGAAGCAAAGGCTCCTCTGGGCCTCAACCAGTGTAAAGAATCCTGCCTATTCTGACACCTTATATGTTGCTCCTCTTATTGGACCCGACACtgtaagccatcatttttttcactttctcaatttgtttataattatgatcgggttgatcttaaagctaatattattagctttaatggacctgtttgttgtctggccttgtttgttctaaaaaacttaaaaaccaaagtttcctttgctgcatctcacatagcaataccttcttactttaca

upper sequence: AT5G13420.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G19380.1 (Glycine max), 5'ss of exon 5
AGGTGCCAAGAAACAGAGACTTCTCTGGGCATCAACAAGTGTAAAGAACCCAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatc--tttttgtttgtgttgaagtcaataggctgtattaacgct---ttggaagtatattca---tagtttttgtgggtgtgatt-tag----------------------------------------------------------------
 ||  ||||||| || || || |||| ||  ||||| | |||||||||||| || || ||||||||||||||||| ||| |||| || |||||| |||||||||| ||||  |||||   | || | |  |  |  |  |   ||   | |    |  ||  ||||| |   ||| |||  |||   || || | |                                                                
GGGGACCAAGAACCAAAGGCTCCTCTCGGTCTCAACCAATGTAAAGAACCCTGCCTATTCTGACACCTTATATGTTGCTTCTCTTATTGGACCTAACACTgtaagccatcattttttcactttgctaatttttaatgattaggtttgagttaatctaaaaaaatattaagattagctttaatggacttgtttgttgtttggccttatttttgttaaagaaacttaaaaaccacaatttcctttgatgtatcttatcatag

upper sequence: AT5G13420.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 5'ss of exon 6
AGGTGCCAAGAAACAGAGACTTCTCTGGGCATCAACAAGTGTAAAGAACCCAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatctttttgt-----ttgtgttgaagt---caataggctgtattaacgctttg-gaagtatattcatagtttttgtgggt-gtgatttag-------------------------------------
|||||||||||||||||| || || ||||| ||||| ||||| ||||| || || ||| |||||||  |||||||  ||||||| || ||||| ||||| || || | |||| |  |      |  |||| | |   || ||     | | | |    |  |||   |||  |   |||   |     ||    ||                                      
AGGTGCCAAGAAACAGAGGCTGCTGTGGGCTTCAACCAGTGTCAAGAATCCTGCCTACCCTGACACACTATATGTGTCTCCTCTTATTGGACCCGACACGgtgagccttcttatattgcaacctcagttggatttggcagtaattgttgtcagcatcctaagaaagttatctaccatttacttaaacagttccataaataaggtccataatttactgccaacttcctttttcag

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|125074125|gb|EL138199.1|EL138199
EST:     ACACCTTATATGTCGCTCCTCTCATCGGACCTGACACT                         GTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAAT
genomic: ACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatc ... tgtgatttagGTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAAT
EST: gi|164092789|gb|ES081126.1|ES081126
EST:     CGGACCTGACACT                         GTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAATA
genomic: CGGACCTGACACTgtaagtcatc ... tgtgatttagGTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAATA
EST: gi|86082459|gb|DR378218.1|DR378218
EST:     CWGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACT                         GTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAATA
genomic: CAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatc ... tgtgatttagGTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAATA
EST: gi|86079131|gb|DR374888.1|DR374888
EST:     CAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACT                         GTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAATA
genomic: CAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatc ... tgtgatttagGTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCAGATCATGGAATA
EST: gi|164203416|gb|ES037033.1|ES037033
EST:     CAGCTTACTCTGACACCTTATATGTCGCTCCTCTCGTCGGACCTGACACT                         GTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCA
genomic: CAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatc ... tgtgatttagGTATCAACCATGCCGGATCAAGCCCTGGAAGCATTCGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTGCCAAGAAACAGAGACTTCTCTGGGCATCAACAAGTGTAAAGAACCCAGCTTACTCTGACACCTTATATGTCGCTCCTCTCATCGGACCTGACACTgtaagtcatctttttgtttgtgttgaagtcaataggctgtattaacgctttggaagtatattcatagtttttgtgggtgtgatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC