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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcag

Basic information

species Arabidopsis thaliana
transcript AT3G16785.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G16785.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaa-cataaccattgtgtttttcag
  |||| || ||||||||||||||||| || |||||| | |  || |||||||| || ||||| || ||||| |||||||| |||||||| ||||| ||||||   |  | |   |  |   |  |  ||       || || ||  | ||||  ||||  | ||    | | |||| |||
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcata-------gtcttccccttcattattgtaaataaaataccttttttttccag

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G066485_T01 (Zea mays), 5'ss of exon 10
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcag
  |||| || ||||||||||||||||| || |||||| | |  || ||||||||||||||||| || ||||| |||||||| |||||||| ||||| ||||||  |  |||    | |            |||| || |  |         ||   |||  |     || | | ||||||
ATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTATGGCCCACCTTGCCGTGATGTAGCGAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtt-gcttatatccttgtgg----------tctgcttatcatagaaagcggtaaactaa--ttgtttttttttctttcag

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA09G04620.1 (Glycine max), 5'ss of exon 11
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcaccc-atacttctttaactt-----tcttctatctgtttg---tttttcctgttattaccgtaacataaccattgtgtttttcag---------
  |||| || ||||||||||||||||| ||||||||  | ||||||||||||||||||||  | ||||||||||||||||| || ||||| ||||| ||||||   |  ||  | |  |  | |     ||||  | |  | ||    | ||||| |  |  |   |    ||  | | | ||||| |          
ATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGGGGACCACCTTGCCGTGACATTGCTAGGCACTTTGTTCAGCGATGGAATTATGCCAAGgttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcag

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA15G16270.1 (Glycine max), 5'ss of exon 11
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcaccc-atacttctttaactt-----tcttctatctgtttgtttttcctgttattaccgtaacata---accattgtgtttttcag---------
  |||| || ||||||||||||||||| ||||||||  | ||||||||||||||||||||  | ||||||||||||||||| || ||||| ||||| ||||||   |  ||  | |  |  | |     ||||  | |  | || |  |  |  |||   |  || |||   |  | | | ||||| |          
ATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGGGGACCACCTTGCCGTGACATTGCTAGGCACTTTGTTCAGCGATGGAATTATGCCAAGgttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcag

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 5'ss of exon 12
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgtt--------cacc-catacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcag
  |||| || ||||| |||||||| || ||||||||  |||||||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| ||||||        |||  |||||| | |     |||||  |   || |  |   ||| ||||  |   || | || |||  | || | |||
ATATCCTCGTATGCCATGGCATGACGTCCATTGTGCCCTATGGGGACCGCCTTGTCGTGATGTAGCTAGGCACTTTGTTCAGCGTTGGAACTATGCAAAGgttgatgtcttcactacatactccctagttcttctttcaaaagtataataaaccttttatctc---aatacaagcatacttttctgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA