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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTCTTCCTTTCAAGGAGAAGAGGATTTGTGCGCATAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaaagagttgctcacaaagtgttatgctctatgtagttgtctttatgtacctgaaactctcaaactaatcagttggtcagaaacgtgattcgaattttgtaccgtttctgcattccagttttacgtttcatatgtgcgtttcttttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G51520.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G21960.2 (Glycine max), 5'ss of exon 6
AATGTCTTCCTTTCAAGGAGAAGAGGATTTGTGCGCATAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaaagagttgctcacaaagtgttatgctct-atgtagttgtctttatgtacctgaaactctcaaactaatcagttggtcagaaacgtgattcgaattttgtaccgtttctgcattccagttttacgtttcatatgtgcgtttcttttgcag
| || ||| |||  |   || ||||||||||| |||||||| |||||  |||| |  || ||||||||||| ||||||||||||||||||      |    |||  ||   | | ||||  ||| | | |    ||       |  ||    |  |||  || | || ||   | ||   | |  | ||  |                                                     
ATTGCCTTTCTTAAATCAAGGAGAGGATTTGTCCGCATAGCAATGGAGAAGGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAGgtattt---atttcttgtccattta-tcttatattcttaaggaaaaatcacgcaccatttgctgattccaagata-ttagctgcagaaaattcttaaactaaaat-----------------------------------------------------

upper sequence: AT3G51520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA09G32790.1 (Glycine max), 5'ss of exon 6
AATGTCTTCCTTTCAAGGAGAAGAGGATTTGTGCGCATAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaaagagttgctcaca-aagtgttatgctctatgtagttgtctttatgtacctga--aactctcaaactaatcagttggtcagaaacgtgattcgaattttgtaccgtttctgcattccagttttacgtttcatatgtgcgtttcttttgcag
| || ||  |||  |   ||||| |||||||| |||||||| |||||  | || |  || ||||||||||| ||||||||||||||||||       |   |||  ||   |  | |||| || || | |    ||||   | |  |     |||| || | ||    | ||   | ||  || |  | ||  |                                                     
ATTGCCTATCTTAAAGCAAGAAGGGGATTTGTCCGCATAGCAATGGAGAAAGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttcttta---ttgtccatgtatattttattct-taaggaaaaatcttgccgcattttgctgactcccagatta----gctgcagaaaactgttaaactaaaatg----------------------------------------------------

upper sequence: AT3G51520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 6
AATGTCTTCCTTTCAAGGAGAAGAGGATTTGTGCGCATAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaaagagttgctcacaaagtgttatgc--tctatgtagttgtctttatgtacctgaaactctcaaactaatcagttggtcagaaacgtgattcgaattttgtaccgtttctgcattccagttttacgtttcatatgtgcgtttcttttgcag
  || ||||||       |||| ||||||||| ||||||||||||||   |||  | ||  |||||||||| ||||||||||||||||||   |       || | ||| | || ||  ||  |||   |||  | ||   | || |   |  | |||      ||  ||   ||      | |||  ||                                                        
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgtttt--cttccccaccaggtatttggccatctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgt-taatttcaa--------------------------------------------------------

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|164001904|gb|ES107952.1|ES107952
EST:     CCAGTAATTCTGCTTTGGTCAG                         GCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
genomic: CCAGT-ATTCTGCTTTGGTCAGgtaggggaaa ... tcttttgcagGCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
EST: gi|86076964|gb|DR372721.1|DR372721
EST:     TAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAG                         GCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
genomic: TAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaa ... tcttttgcagGCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
EST: gi|86080043|gb|DR375800.1|DR375800
EST:     TAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAG                         GCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
genomic: TAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaa ... tcttttgcagGCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
EST: gi|124744729|gb|EH835891.1|EH835891
EST:     CTGCTTTGGTCAG                         GCACGCGTGTACAAATGGTGGAAG
genomic: CTGCTTTGGTCAGgtaggggaaa ... tcttttgcagGCACGCGTGTACAAATGGTGGAAG
EST: gi|116424222|gb|EG466814.1|EG466814
EST:     TAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAG                         GCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA
genomic: TAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaa ... tcttttgcagGCACGCGTGTACAAATGGTGGAAGCCGGATTGTGATCTCTATCTTAAACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGTCTTCCTTTCAAGGAGAAGAGGATTTGTGCGCATAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaaagagttgctcacaaagtgttatgctctatgtagttgtctttatgtacctgaaactctcaaactaatcagttggtcagaaacgtgattcgaattttgtaccgtttctgcattccagttttacgtttcatatgtgcgtttcttttgcag

- - - - - - - - - - - - - - - - - - - -  CATGGA