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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatatatgcttggaaaacaacatacttgatctctatagaagtttacttagtgacatttctctgtgtttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTGTCGCTGACCCGACTTTTG

Basic information

species Arabidopsis thaliana
transcript AT5G52970.1
intron # 3
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|163996652|gb|ES055980.1|ES055980
EST:     CTATCCCGTTACACCTG                         GACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTG
genomic: CTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTG
EST: gi|124966855|gb|EL040931.1|EL040931
EST:     TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAAGGTGGATGATAGCACAATTGTGTTT
genomic: TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCA-GGTGGATGATAGCACAATTGTGTTT
EST: gi|124715159|gb|EH806561.1|EH806561
EST:     TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGG
genomic: TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGG
EST: gi|124889806|gb|EH968708.1|EH968708
EST:     TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGG
genomic: TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGG
EST: gi|125307315|gb|EL321400.1|EL321400
EST:     ATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTG
genomic: ATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTG
EST: gi|124910722|gb|EH984802.1|EH984802
EST:     ATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTG
genomic: ATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTG
EST: gi|125210796|gb|EL225750.1|EL225750
EST:     TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGGTGGATGATA
genomic: TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATA
EST: gi|124865612|gb|EH950049.1|EH950049
EST:     TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTG
genomic: TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTG
EST: gi|124776677|gb|EH866754.1|EH866754
EST:     TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG                         GACTAGCAATCAAAGATTTCTGGCAGGTGGA
genomic: TACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTGgtatgatata ... tttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacttgatctctatagaagtttacttagtgacatttctctgtgtttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTGTCGCTGACCCGACTTTTG
   acttgat  putative branch site (score: 5)
                     tttactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatatatgcttggaaaacaacatacttgatctctatagaagtttacttagtgacatttctctgtgtttgcaacagGACTAGCAATCAAAGATTTCTGGCAGGTGGATGATAGCACAATTGTGTTTGTCGCTGACCCGACTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA