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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaatattggaacaactcttagattaccacgaactttaggtttagtagagttccttgaaattcttggacctaattaaaacttgtatttgcccccaaatcaaatcaatttcttggcttaatcttgacacttttattggttgttttgtttttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGCATTTGCCTTGACATTTTGAAAGAACAATGGAGCCCTGCCCTCACCATTT

Basic information

species Arabidopsis thaliana
transcript AT5G41700.2
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|125162570|gb|EL189340.1|EL189340
EST:     TCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
genomic: TCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
EST: gi|125067045|gb|EL133693.1|EL133693
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
EST: gi|125029701|gb|EL101970.1|EL101970
EST:     TCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
genomic: TCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
EST: gi|124990288|gb|EL062557.1|EL062557
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACG
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACG
EST: gi|124978993|gb|EL052099.1|EL052099
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAG
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAG
EST: gi|124734987|gb|EH826389.1|EH826389
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAA
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAA
EST: gi|125054731|gb|EL125279.1|EL125279
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
EST: gi|125259365|gb|EL273450.1|EL273450
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGA
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGA
EST: gi|125033004|gb|EL105273.1|EL105273
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCA
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCA
EST: gi|163996451|gb|ES127935.1|ES127935
EST:     CTATCCATTCAAACCACCAAAG                         GTTGCATTTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAG
genomic: CTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCA-TTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAG
EST: gi|125266157|gb|EL280242.1|EL280242
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTT-CACCCTAAT
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAAT
EST: gi|124897032|gb|EH973246.1|EH973246
EST:     TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAG-TGTTTCACCCTAATATCAACAGCAACGGAAGC
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGC
EST: gi|124854724|gb|EH939161.1|EH939161
EST:     TTCTCGTTACCATTCACTTCCTTCCGGACTATCCATTCAAACCACCAAAG                         GTTGCATTTAGGACGAAGGTGTTTCA
genomic: TTCTCGTTACCATTCACTTCCCTCCGGACTATCCATTCAAACCACCAAAGgtattcaata ... ttatttgcagGTTGCATTTAGGACGAAGGTGTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttcttggcttaatcttgacacttttattggttgttttgtttttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGCATTTGCCTTGACATTTTGAAAGAACAATGGAGCCCTGCCCTCACCATTT
                tcttgac  putative branch site (score: 3)
                                     ttttgtttttattt  putative PPT
                                  ttgttttgtttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcaatattggaacaactcttagattaccacgaactttaggtttagtagagttccttgaaattcttggacctaattaaaacttgtatttgcccccaaatcaaatcaatttcttggcttaatcttgacacttttattggttgttttgtttttatttgcagGTTGCATTTAGGACGAAGGTGTTTCACCCTAATATCAACAGCAACGGAAGCATTTGCCTTGACATTTTGAAAGAACAATGGAGCCCTGCCCTCACCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC