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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgactttatcaaactctttttttttttttccgtttcttgtcaaatcaatctctgatcttgatcgatattttatcacttaaccgatgctgatcatatcataatcatgtgtatatattggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAGTGTATGGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTT

Basic information

species Arabidopsis thaliana
transcript AT5G02580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G02580.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 1
gtacgactttatcaaactctttttttttttttccgtttcttgtcaaatcaatctctgatcttgatcg-atattttatcacttaaccgatgctgatcatatcataatcatgtgtatatattggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAGTGTATGGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTT
                    ||| ||| ||||  ||    |    |   ||  ||||||  |||  | |||| |   |||  |    ||    || |||| || || ||   ||| | |       ||||||| | | ||||||| || |||||  ||||||||||| ||||||||||||| ||||| ||||| | ||| ||||| ||||| |||||| | || || |
--------------------tttgtttctttttggtggaatacatatataagttctgatgatgaaggtatatatatgcacaca-taaatatatataatataattataatacatatgtgt-------agGTGCACCGTCTGATAGAGGAGTGTATCCTATTCAACATGAGCAAAGAAGAGTGCATGGAAGCTCTTTCCAAACATGCAAATATCAAGCCTGTTATTACCT

upper sequence: AT5G02580.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G33110.1 (Glycine max), 3'ss of exon 1
gtacgactttatcaaactctttttttttttttccgtttcttgtcaaatcaatctctgatc--ttgatcgatattttatcacttaaccgatgctgatcatatcataatcatgtgtatatattggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAGTGTATGGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTT
                   |||| |||  |||  ||  | |    |   ||  ||||||    |||  | ||| ||  ||   |    ||         || ||||||||   || ||||    || ||||||| | | ||||||| || |||||  ||||||||||| ||||||||||||| ||||| ||||| | ||| ||||| ||||| |||||  | || || |
-------------------ttttgtttccttttggtggcatacgtatataagttctgatgaagtgaagggtatatttgcatacatataatata------attataatcata-atacatatg---tgtagGTGCACCGTCTGATAGAGGAGTGTATCCTATTCAACATGAGCAAAGAAGAGTGCATGGAAGCTCTTTCCAAACATGCAAATATCAAGCCGGTTATTACCT
















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|86029377|gb|DR325130.1|DR325130
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|86029380|gb|DR325133.1|DR325133
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|86029379|gb|DR325132.1|DR325132
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|86076807|gb|DR372564.1|DR372564
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|86029378|gb|DR325131.1|DR325131
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|19874569|gb|AU235400.1|AU235400
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|86029381|gb|DR325134.1|DR325134
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
EST: gi|86029382|gb|DR325135.1|DR325135
EST:     AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTG                         GTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG
genomic: AAGTATTTATGGGTGATCATAATAGCTCGCAAGCTTCTTACATCCATTTGgtacgacttt ... ttggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcacttaaccgatgctgatcatatcataatcatgtgtatatattggttgcagGTGCATCATTTGATAGAAGAATGTATAGTATTCAACATGGGCAAAGAAGAGTGTATGGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTT
               tgctgat  putative branch site (score: 3)
                       atatcataat  TA-rich tract