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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcattactttattgatatgagaagctaaaggagcttgtttctgttaaatttatcctttcagttaaacattgtcaaatatcttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G24200.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G24200.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA02G36530.1 (Glycine max), 5'ss of exon 7
GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtat-----tgcattactttattgatatgagaagctaaaggagct-tgtttctgttaa--atttatcctttcagttaaacattgtcaaatatcttgcag-
|| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||||||||| || || |||||||     |  |   || |     |||      ||| |   |   | |  |  | ||  ||  |  || |  |     ||     ||   |     || 
GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAGgtataactgtatacagctatgcatttatttctttctatacctgtaatatccccataaatcatcaaaactctaggcctcccacccaaaagatttgcttagc

upper sequence: AT2G24200.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA16G19350.1 (Glycine max), 5'ss of exon 7
GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcattact---ttattgatatgagaagctaaaggagcttgtttctgttaaatttatcctttcagttaaacattgtcaaatatcttgcag-------
|| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||| ||||| || || |||||||  ||||||     |||  ||               |  |  |    | |  |  | ||| | |    | |  |||   |  || |   |        
GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAGgtataacattacgcagctatgcattctttccatccttataaatcataaaagctccaggtctccctcccaaaagat-ttgcttagcatttaaaattttattt

upper sequence: AT2G24200.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA17G08150.1 (Glycine max), 5'ss of exon 7
GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcattact---ttattgatatgagaagctaaaggagcttgtttctgttaaatttatcctttcagttaaacattgtcaaatatcttgcag-------
|| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||| ||||| || || |||||||  ||||||      ||  ||               |  |  |    | |  |  | ||| | |    | |  |||   |  || |   |        
GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAGgtataacattacgcagccatgcattctttccatccttataaatcataaaagctccaggtctccctcccaaaagat-ttgcttagcatttaaaattttattt

upper sequence: AT2G24200.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA19G22730.1 (Glycine max), 5'ss of exon 7
GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcattactttattga---tatgagaagctaaaggagcttgtttctgttaaatttat-cctttcagttaaacattgtcaaatatcttgcag-----
|| || ||||||||||| || ||| | || || || ||||||||||| ||||||||||||||||| || |  || |||||||     ||      |||   | |   |   | |   |  |  |   ||| |  | ||| |  || |  | |||  |  ||  ||   |  |      
GTTAATAACACAGATGCAGAGGGTAGGCTTACCCTGGCAGATGCTCTGGTGTATGCTTGTAACCAGGGTGCTGAAAAGgtatgctgctatgaatctgaatctttctaatatttacataaatcataattgtgaggtgtatactctttaagttaactctaccagttagagttaaccccta

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|47829652|gb|CK119336.1|CK119336
EST:     CTTGTAACCAAGGCGTCGACAAG                         ATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
genomic: CTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
EST: gi|116409488|gb|EG452080.1|EG452080
EST:     TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG                         ATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
genomic: TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
EST: gi|116409481|gb|EG452073.1|EG452073
EST:     TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG                         ATTGTTGGCCTCGCTACTTTGACCGGGGCCTGTGTTATTGCCCTTGGAACT
genomic: TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
EST: gi|86087145|gb|DR382904.1|DR382904
EST:     TGTATGCTTGTAACCAAGGCGTCGACAAG                         ATTGTTGMCCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
genomic: TGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
EST: gi|116409618|gb|EG452210.1|EG452210
EST:     TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG                         ATTGTTGACCTCGCTACTTTGACCG
genomic: TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCG
EST: gi|116409637|gb|EG452229.1|EG452229
EST:     TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG                         ATTGTTGACCTCGCTACTTTGACCG
genomic: TAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCG
EST: gi|124766773|gb|EH856903.1|EH856903
EST:     CACTCGCAGATACTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG                         ATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT
genomic: CACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcatt ... tatcttgcagATTGTTGACCTCGCTACTTTGACCGGGGCCTGTGTTATTGCTCTTGGAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAGgtattgcattactttattgatatgagaagctaaaggagcttgtttctgttaaatttatcctttcagttaaacattgtcaaatatcttgcag

- - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - -  CAGATG