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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcacatgttaaaagtttcaacatttactctgttttgctctgtttttgtcgtttggtattgacatatgtctcttgtttcttttgatatctggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAAGAATCTAGCGAGCACAAGCTCTTCAAAGCTAGGTAACGAATCCTCTCAT

Basic information

species Arabidopsis thaliana
transcript AT3G16500.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G16500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G43050.2 (Glycine max), 3'ss of exon 2
cttcacatgttaaaagtttcaacatttactctgttttgctctgtttttgtcgtttggtattgacatatgtctcttgtt--tcttttgatatctggttcaa-agAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAAGAATCTAGCGAGCACAAGCT---CTTCAAAGCTAGGTAACGAATCCTCTCAT
 ||       |   ||  |      |||| | ||||  || |    || || |     | | ||   | |  |||||    |  || | |        || ||||||||||||| |||||||||||| ||||| ||  ||||||| ||||| ||||| ||  | ||||  |||    |||| |||| |   | |   ||||     
tttttttaacttttagcct-ggttcttac-cagtttcactgtacactt-tcatgcataacttaccatttttccttgtggacccattaacaaacaaacaaacagAACTGCTCCTGCTCCAGTGGTGGGGTGGCCCCCAATTCGTTCATTCAGGAAGAACCTTTCAAGCAGCAGCAGTGCTTCTAAGCCAC-CACCACCTCCTGAG--

upper sequence: AT3G16500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G02350.1 (Glycine max), 3'ss of exon 2
cttcacatgttaaaagtttcaacatttactctgttttgctctgtttttgtcgtttggtattg-acata---tgtctcttgtttcttttgatatc--tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAAGAATCTAGCGAGCACAAGCT---CTTCAAAGCTAGGTAACGAATCCTCTCAT
         ||   | ||| ||| ||||  ||| ||    |   |||    |||   | |    | ||   |  |  ||  | ||| ||    |  |     | ||||||||||||| |||||||||||| ||||| ||  ||||||| ||||| ||||| || || ||||  |||    |||| |||| |  |   || ||       
------tcttttgtatttttaacttttagcctggttcttaccagtttcactgttcactttcatgcctaacttaacattttctccttgtggacccattaacaaacagAACTGCTCCTGCTCCAGTGGTGGGGTGGCCCCCAATTCGTTCCTTCAGGAAGAACCTTGCAAGCAGCAGCAGTGCTTCTAAGCCACCTCCTGAGTCTCAG---

upper sequence: AT3G16500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G01800.1 (Glycine max), 3'ss of exon 1
cttcacatgttaaaagtttcaacatttactctgttttgctctgtttttgtcgttt--ggtattgacatatgtctcttgtttcttttgatatctggttcaaa---gAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAAGAATCTAGCGAGCACAAGCTCTTCAAAG-CTAGGTAACGAATCCTCTCAT
       || | |   |   |   |||  |||  || |    ||  ||||  |||    | || |   ||| ||    |||  |       |      |||   |||||||| | |||||||| ||||||||||||||  ||||||| ||||| |||||  | || ||   |||| |||| ||  ||| ||  |        ||  
-----tgtgatgattctgatatgcttttgtcttcttagggtagtgcttgttatttttactgtttatccatgcctaactttttgtacatgggcccaccaaaaacagAACTGCTTCAGGTCCAGTAGTGGGTTGGCCTCCAATTCGTTCCTTCAGGAAGAACATTGCAAGTGGAAGCACTTCTAATTCTAAGTTGCCTTCTGGGTCC-

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|86048602|gb|DR344357.1|DR344357
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
EST: gi|86048600|gb|DR344355.1|DR344355
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGA
EST: gi|86048601|gb|DR344356.1|DR344356
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGC-TCCGGTTCGTTCGTTCAGAAA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
EST: gi|86048608|gb|DR344363.1|DR344363
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTTCGTTCGTTCAGAA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTT-CGTTCGTTCAGAA
EST: gi|86048613|gb|DR344368.1|DR344368
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTSGTTCGTTCAGAAA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
EST: gi|86048607|gb|DR344362.1|DR344362
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
EST: gi|86048598|gb|DR344353.1|DR344353
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGG
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGG
EST: gi|86048611|gb|DR344366.1|DR344366
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
EST: gi|86048612|gb|DR344367.1|DR344367
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGTGGTGGGTTGGC-TCCGGTTCGTTCGTTCAGAA-
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAA
EST: gi|86048606|gb|DR344361.1|DR344361
EST:     TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAG                         AACTGCTCCTGGTCCAGGTGGTGGGTTGGCCTCC
genomic: TTCTCTCCTTCCAACAAAACCACTTCTGTTCCTCACATCTCACAGAAAAGgtataatctc ... tggttcaaagAACTGCTCCTGGTCCAG-TGGTGGGTTGGCCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcgtttggtattgacatatgtctcttgtttcttttgatatctggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAAGAATCTAGCGAGCACAAGCTCTTCAAAGCTAGGTAACGAATCCTCTCAT
                                   ttttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcacatgttaaaagtttcaacatttactctgttttgctctgtttttgtcgtttggtattgacatatgtctcttgtttcttttgatatctggttcaaagAACTGCTCCTGGTCCAGTGGTGGGTTGGCCTCCGGTTCGTTCGTTCAGAAAGAATCTAGCGAGCACAAGCTCTTCAAAGCTAGGTAACGAATCCTCTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - tcaacat
- - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - cgtttgg