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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcag

Basic information

species Arabidopsis thaliana
transcript AT5G39740.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 5
CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtga-----tcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcag---------
| ||||| ||||| ||||||||||||||||||||||| || || |  ||  ||||| | ||||| ||||| || || ||||||   |   |     | ||| | || ||  ||             ||     | ||   |||| | | || || |||  ||    |||||| |            
CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatatttaaatttattctgcttgctgtttttttttgtgatattg--ctttgggtgaacaattgag-catttgtgatgattttctgttatcag
















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|164064961|gb|ES119285.1|ES119285
EST:     TGGATGATGTAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTA
genomic: TGGATGATG-AGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTT-
EST: gi|125288919|gb|EL303004.1|EL303004
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCA
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCA
EST: gi|125207196|gb|EL222150.1|EL222150
EST:     GCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|125034575|gb|EL106844.1|EL106844
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|164191864|gb|EL977964.1|EL977964
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGG
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGG
EST: gi|116398433|gb|EG441025.1|EG441025
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|164128351|gb|ES100101.1|ES100101
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGA-GGACTTTTCTGTGGAACCAACTGATTCCAGAAGACC
EST: gi|164209527|gb|ES079920.1|ES079920
EST:     TGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: TGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|125158069|gb|EL186840.1|EL186840
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|163972979|gb|ES099547.1|ES099547
EST:     GGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|163972920|gb|ES197012.1|ES197012
EST:     GGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTT-C
genomic: GGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|164097969|gb|EL977361.1|EL977361
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCA
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCA
EST: gi|124764489|gb|EH854619.1|EH854619
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGA
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGA
EST: gi|116398349|gb|EG440941.1|EG440941
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|124841955|gb|EH926392.1|EH926392
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCT
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcag

- - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - -  GCTGGA