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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaattccccccaatcttcgaatataattctcagttgattataaacagtctctgtatccttatatgcttaatgcttacgcatacttaaaactgcag

Basic information

species Arabidopsis thaliana
transcript AT3G53580.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA19G35780.1 (Glycine max), 5'ss of exon 7
AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat---tccccccaatcttcgaatataattctcagt----tgattataaacagtctctgtatccttatatgcttaatgc----ttacgcatacttaaaactgcag
| |||||  | || |||||    ||||| |||||||||||||| |||||||| |||||||||  | ||||   |||  |   | | | | ||| ||| | | |    |  ||      ||| ||    | | |  |   || ||         | |||  ||     |||||
AGTTTGTGCAAGTATTATCTAACTCTCACTTGAAAATGCGTGTTTGGGAGCGGGGAGCAGgttagaaaatctatccatctcgtgtcctattattattgttactgcagttgttggggtaagtttcaaggtgcctcaaaattttatatgggagagctcatgttttgttgtgcag
















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|124771390|gb|EH861520.1|EH861520
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGG
EST: gi|125253821|gb|EL267906.1|EL267906
EST:     TATCACGTTCTCATTTGAAAATGCGTGCGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAA
genomic: TATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAA
EST: gi|164210826|gb|ES169349.1|ES169349
EST:     GTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGG
genomic: GTCTTATCACGTTCTCATTTGAAAATGCGTGTGT-GGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGG
EST: gi|86082085|gb|DR377844.1|DR377844
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
EST: gi|86080834|gb|DR376591.1|DR376591
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
EST: gi|86033409|gb|DR329162.1|DR329162
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAS-AG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
EST: gi|86078439|gb|DR374196.1|DR374196
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
EST: gi|116478499|gb|EG521091.1|EG521091
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
EST: gi|124789106|gb|EH878785.1|EH878785
EST:     CGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: CGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
EST: gi|116478497|gb|EG521089.1|EG521089
EST:     GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG                         GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG
genomic: GGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaat ... aaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAGgtccgcaaattccccccaatcttcgaatataattctcagttgattataaacagtctctgtatccttatatgcttaatgcttacgcatacttaaaactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG