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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAGgtgagctatgttctcttttatgacttggtcatcgctgtcctgcaattagttaaagatcatatgacatagtttggttgatcaatcagaatctctgtcccac...

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 9
CTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAGgtga-gctatgttctcttttatgacttggtcatcgctgtcctgcaattagttaaagatcata-tgacatagtttggttgatcaatc--agaatctctgtcccac
 |||||  | || ||||||||||||||||| ||||||||||| || || || ||  | | | | ||    || || ||||||   || || || |||||||||| ||  ||   | |  ||    |  ||  ||  | || |   || | ||     | | |    | || |||  |  || | |   ||||  | |||     
TTGGCTCTTATCTTATTATGAACCTGCAATCGAGTACTTGGCTACTTCTAGAACCCTACCACGACTAGTAGAGGTTGTTAAGAGTTCAACAAAAGAAAAGgtgatgccctgccttttggtactcttgagt--tcattttcttttcatcaattttgtcttacaactgcctatttttatatattatttctagaagatgtgtata--
















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|125253864|gb|EL267949.1|EL267949
EST:     GACTAAGGAAAAG                         GTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTTCCAAAAGGTACA
genomic: GACTAAGGAAAAGgtgagctatg ... tatcttacagGTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTTCCAAAAGGTACA
EST: gi|125147863|gb|EL181861.1|EL181861
EST:     GGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAG                         GTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCT
genomic: GGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAGgtgagctatg ... tatcttacagGTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCT
EST: gi|125221280|gb|EL235365.1|EL235365
EST:     CACTCGACTAAGGAAAAG                         GTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTTCCAAAAGGTACA
genomic: CACTCGACTAAGGAAAAGgtgagctatg ... tatcttacagGTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTTCCAAAAGGTACA
EST: gi|125152238|gb|EL183978.1|EL183978
EST:     GGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAG                         GTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTT
genomic: GGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAGgtgagctatg ... tatcttacagGTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTT
EST: gi|86031301|gb|DR327054.1|DR327054
EST:     GGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAG                         GTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTTCCAAAAGGTACA
genomic: GGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAGgtgagctatg ... tatcttacagGTTGTCAGGGTGGTCATATTGACATTCAGGAACCTTCTTCCAAAAGGTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGCTTCTGTCCTATTATGAACCTGCAATAGAGTACTTGGCAACATCGAGGACAATGCAAAGGCTCACGGAAGTGGTTAAGCACTCGACTAAGGAAAAGgtgagctatgttctcttttatgacttggtcatcgctgtcctgcaattagttaaagatcatatgacatagtttggttgatcaatcagaatctctgtcccac

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgctgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctgtc