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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagagttatactattatttggtatagatgttgtgtgagttttggcacttaaagtaacaaacttgcgtctctgttacttgttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAGATGCAATTGCTAATGCTCTTAAAGGATCAGACCTTGTTTTCATAACTGC

Basic information

species Arabidopsis thaliana
transcript AT5G55280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 2
-----------------------------------gttagtagagttat--actattatttggtatagatgttgtgtgagttttggcacttaaagtaacaaacttgcgtctctgttacttgttt-taat--agGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAGATGCAATTGCTAATGCTCTTAAAGGATCAGACCTTGTTTTCATAACTGC
                                   || | | |  ||     ||| | | | || |   || ||  |   |||||  |  |  ||       |||   |     || | || |  | ||  ||| || || || || || ||| | || |||||||||||||| ||||||| |||||| |||||| |||||||||||||||||||  | || || ||||| ||
gtcaggcactctacttgtatagtttttgctatgatgtgatttgtttttgtggctactgtcttgtttctttgctgaatt--ttttgagaaattgaggggtggcctttgattcaaattgcctgatagtgatgcagGTACGGGCGGGAATCCACTTTTGGGGGAACAAGCTGCAGAGGAATCAAGAGATGCTATTGCTGATGCTCTTAAAGGATCAGATTTGGTGTTTATAACGGC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------gttagtagagttatactattatttggtatagatgt-tgtgtgagttttggcacttaaagtaacaaacttgcgtctctgttacttgttttaa---tagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAGATGCAATTGCTAATGCTCTTAAAGGATCAGACCTTGTTTTCATAACTGC
                                                     |   || |  | | | || || || | || |||| |||||| ||     ||||  ||      | |||   |    ||| |||| |  |     ||| |||||||| || || ||| | || ||||||||||| || ||||||||||| || ||||| ||||||||| ||||||||||  | || ||  |||||||
gtcaggaagttgcattttatgcctagggggttcctttgtacttgattataacatgcatatatgt-tgcaatcatgtgatctatatgtgtgtgtgtgtggcttcactccaat--gtgacctttgattcgagttgcttgatagagatgcagGTACTGGTGGGAATCCACTTTTGGGGGAACAAGCTGCTGAGGAATCAAAAGAAGCTATTGCCAATGCTCTTCAAGGATCAGATTTAGTGTTTGTAACTGC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 2
------------------------------gttagtagagttatactatta--tttggtatagatgttgtg-tgagtt--ttggcacttaaagtaacaaacttgcgtctctgttacttgttttaa---tagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAGATGCAATTGCTAATGCTCTTAAAGGATCAGACCTTGTTTTCATAACTGC
                               | |   || || |  |  |   |   || | | |  | || ||| ||  ||| ||  |  ||       |||   |     ||||||| |  |     ||| || ||||| || || ||| | || ||||||||||| || ||||| | |||||| |||||| |||||||||||||||||||  | || || ||||| ||
gtcaggcactctacttgcatagtttttactatgatgtgatttgtttttgtggctacagtcttgtttctttgctgaatttgttgacaaattgaggggtggcctttgattcaaattacttgatagagatgcagGTACAGGTGGGAATCCACTTTTGGGGGAACAAGCTGCGGAGGAATCCAGAGATGCTATTGCTGATGCTCTTAAAGGATCAGATTTGGTATTTATAACGGC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 2
----------------------------------------gttagtagagttatactattat-ttggtatag-atg--ttgtgtgagttt---tggcacttaaagtaa--caaacttgcgtctctgtt--acttgttttaa-------tagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAGATGCAATTGCTAATGCTCTTAAAGGATCAGACCTTGTTTTCATAACTGC
                                         ||  |   |  || |   ||| ||| |||||  ||  ||||||| |  |   ||| |||||   | |  | ||  ||    |   ||  | ||| || |         ||| ||||| || || |||||| | || ||||||||||| || ||||||||||| || ||||||||||||||| |||| || ||  | || ||  |||||||
gtcaggcacttgcattttatgcctaggtggttcctttgtgcttgattatgacatgcatatatgttgctatagtgtgatttgtgtgtgcctgtgtggtacttagcttcattctaatgtgtcctttgattcaagttgcttgagagagatgcagGTACTGGAGGGAATCCGCTTTTGGGGGAACAAGCTGCTGAGGAATCAAAAGAAGCTATTGCTAATGCTCTTCAAGGCTCGGATTTAGTGTTTGTAACTGC

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|86039268|gb|DR335023.1|DR335023
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTT
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTT
EST: gi|86039263|gb|DR335018.1|DR335018
EST:     TCTGCTGAGAACCCACTTCAAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCC
genomic: TCTGCTGAGAACCCACTTCAAA-TTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCC
EST: gi|125140157|gb|EL178547.1|EL178547
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAG
EST: gi|86039251|gb|DR335006.1|DR335006
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039253|gb|DR335008.1|DR335008
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACC-GCTTCTTGG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGG
EST: gi|86039254|gb|DR335009.1|DR335009
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGA
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGA
EST: gi|164027950|gb|ES177778.1|ES177778
EST:     GGAGAACTTTTAACTC-TGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: GGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039257|gb|DR335012.1|DR335012
EST:     TCTGCTGAGAACCCACTTCAAATCTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGA
genomic: TCTGCTGAGAACCCACTTCAAAT-TGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGA
EST: gi|86039272|gb|DR335027.1|DR335027
EST:     TKCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACC-GCTTCTTGGAGAACAAGCTGCAGAAGAAT
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAAT
EST: gi|86039256|gb|DR335011.1|DR335011
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039271|gb|DR335026.1|DR335026
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039249|gb|DR335004.1|DR335004
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAA
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAA
EST: gi|301501112|gb|HO206652.1|HO206652
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039260|gb|DR335015.1|DR335015
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039269|gb|DR335024.1|DR335024
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039270|gb|DR335025.1|DR335025
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCKTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagttttggcacttaaagtaacaaacttgcgtctctgttacttgttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAGATGCAATTGCTAATGCTCTTAAAGGATCAGACCTTGTTTTCATAACTGC
                 aagtaac  putative branch site (score: 2)
                                          cttgtttt  putative PPT
                                       ttacttgttttaata  TA-rich tract