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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGATGTCGACAAACAGCGGGAGGCCAATATCTCCGGCGATGATGCCTTTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattatttctcttctttctgtttgcatcacaatgttgaacatagagtttgatatttttccggtccggacttaaatggatgcatgagtccaattcagtc...

Basic information

species Arabidopsis thaliana
transcript AT3G09740.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09740.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv08s0040g02130.t01 (Vitis vinifera), 5'ss of exon 1
GTACGATGTCGACAAACAGCGGGAGGCCAATATCTCCGGCGATGATGCCTTTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattatttctcttctttctgtttgcatcacaatgttgaacatagagtttgatatttttccggtccggacttaaatggatgcatgagtccaattcagtc
||||||  ||||||| |||  |||   |||| ||||||||||||||||||| |||||||| || |  |   | ||| || | |||||| |||||||  ||||     |   || |||||| |    |       | |   | | |      || |  ||              || | | |  ||     | |   ||||
GTACGACATCGACAAGCAGAAGGATCTCAATGTCTCCGGCGATGATGCCTTCGCTCGTCTTTACGCCGTCGTTGAAGCCGACATCGAGGCCGCTCTTCAGgtccaattccttcctctttccgccctcggtttggtttccgagaaaaccgaggagaagttataaaatgacttgaaattcgctttatctaagctaaatagtc
















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|125276961|gb|EL291046.1|EL291046
EST:     TTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAAGAAAAACAGGGCTGCTGCTGTTG
genomic: TTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGA-GAAAAACAGGGCTGCTGCTGTTG
EST: gi|116431994|gb|EG474586.1|EG474586
EST:     TTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
genomic: TTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
EST: gi|124750257|gb|EH840387.1|EH840387
EST:     CTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTG
genomic: CTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTG
EST: gi|124909769|gb|EH983849.1|EH983849
EST:     CTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAGAAAA-CAGGGCTGCTGCTGTTGCAATG
genomic: CTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
EST: gi|164055042|gb|ES144053.1|ES144053
EST:     GAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAG-AAAACAGGGCTGCTGCTGTTGCAATG
genomic: GAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
EST: gi|116435937|gb|EG478529.1|EG478529
EST:     TTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
genomic: TTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
EST: gi|125030025|gb|EL102294.1|EL102294
EST:     TCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAGAAAAA
genomic: TCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAA
EST: gi|125294844|gb|EL308929.1|EL308929
EST:     CTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
genomic: CTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG
EST: gi|125248854|gb|EL262939.1|EL262939
EST:     GAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAG                         AAAACTGAACTTGTTACGAAGGAGAAAA-CAGGGCTGCTGCTGTTGCAATG
genomic: GAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattattt ... cgatttgcagAAAGCTGAACTTGTTACGAAGGAGAAAAACAGGGCTGCTGCTGTTGCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGATGTCGACAAACAGCGGGAGGCCAATATCTCCGGCGATGATGCCTTTGCTCGTCTCTATGGAGCTTTCGAAACCCAAATCGAGACCGCTCTCGAGgtaattatttctcttctttctgtttgcatcacaatgttgaacatagagtttgatatttttccggtccggacttaaatggatgcatgagtccaattcagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacataga