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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcttaagattgactagtgatcagggtcaatatattgttcatctactgcttatgctactcctaattatatgtgttgatgaaggaccataaccttgtttgattttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTCGCGAAGACAATCTTGTTTTCTCCTTTGAGTTAGGAACAGGCAGTGTTAT

Basic information

species Arabidopsis thaliana
transcript AT3G55520.1
intron # 2
splice site 3'
intron type U2

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|86027819|gb|DR323572.1|DR323572
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
EST: gi|86027820|gb|DR323573.1|DR323573
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
EST: gi|86027816|gb|DR323569.1|DR323569
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
EST: gi|86027814|gb|DR323567.1|DR323567
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGKATCTTGGCTGAAGACGGAAAGGKTTTCGACACTACTC
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
EST: gi|86027813|gb|DR323566.1|DR323566
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
EST: gi|86027818|gb|DR323571.1|DR323571
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGTATCTT
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTT
EST: gi|86027815|gb|DR323568.1|DR323568
EST:     TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATG                         TTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC
genomic: TGCCAAACCTGATGCTATTTCACCCTCTGATGATCTTCCTGTTGTCGATGgtatgttctt ... tttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcctaattatatgtgttgatgaaggaccataaccttgtttgattttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTCGCGAAGACAATCTTGTTTTCTCCTTTGAGTTAGGAACAGGCAGTGTTAT
                                            ttttaac  putative branch site (score: 2)
                                       tttgattttaactta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcttaagattgactagtgatcagggtcaatatattgttcatctactgcttatgctactcctaattatatgtgttgatgaaggaccataaccttgtttgattttaacttagTTCATTATGAGGGTATCTTGGCTGAAGACGAAAAGGTTTTCGACACTACTCGCGAAGACAATCTTGTTTTCTCCTTTGAGTTAGGAACAGGCAGTGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA