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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaccgtcaatatagatctttgtaactttggctacttataaatgtttatcatgtggttttgtcagattttgtaatttctattgttggtttactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTTTCAGCTAAAGGTCTCCAGCTCTTAAGGCGCTATGATAAAAAACCTGAAA

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S51_320V6.1 (Physcomitrella patens), 3'ss of exon 1
caaaccgtcaatatagatctttgtaactttggctacttataaatgtttatcatgtggttttgtcagattt---tgta-atttctattgttggtttactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTTTCAGCTAAAGGTCTCCAGCTCTTAAGGCGCTATGATAAAAAACCTGAAA
      ||  |  |   | | |||    |     | |  |  | |    |  || ||    ||  ||||    |||| | ||  | ||||  |||| |||| |||| ||||||||||| |||||||||||||  |||||||   | |||||| |       |  ||  | || ||  | ||||| |||||  |    || ||||
-tgtgtgtgtacgtgtgtttgtgtgggctgaaagattcctcgaggggagttttg-ggcagagtgggattgatgtgtagaatttgaatgtt--tttattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATCAATAGCACTGGGTTGCAACTGCTGAGGCGATATGACCACCGTCCCGAAA
















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|47832017|gb|CK121701.1|CK121701
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|152033932|gb|BP820357.2|BP820357
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031310|gb|DR327063.1|DR327063
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031302|gb|DR327055.1|DR327055
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|116433606|gb|EG476198.1|EG476198
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|116433595|gb|EG476187.1|EG476187
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031298|gb|DR327051.1|DR327051
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACAC-AAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031307|gb|DR327060.1|DR327060
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031303|gb|DR327056.1|DR327056
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|163967732|gb|ES057313.1|ES057313
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACAC
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACAC
EST: gi|86031311|gb|DR327064.1|DR327064
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031308|gb|DR327061.1|DR327061
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|125195193|gb|EL210147.1|EL210147
EST:     CCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: CCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031304|gb|DR327057.1|DR327057
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031313|gb|DR327066.1|DR327066
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031315|gb|DR327068.1|DR327068
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031316|gb|DR327069.1|DR327069
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GNATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031312|gb|DR327065.1|DR327065
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031300|gb|DR327053.1|DR327053
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
EST: gi|86031317|gb|DR327070.1|DR327070
EST:     TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG                         GTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT
genomic: TTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAGgttggtgata ... tactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcatgtggttttgtcagattttgtaatttctattgttggtttactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTTTCAGCTAAAGGTCTCCAGCTCTTAAGGCGCTATGATAAAAAACCTGAAA
                                           tttacttt  CT-rich tract
                     attttgtaatttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaccgtcaatatagatctttgtaactttggctacttataaatgtttatcatgtggttttgtcagattttgtaatttctattgttggtttactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTTTCAGCTAAAGGTCTCCAGCTCTTAAGGCGCTATGATAAAAAACCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
caaaccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattttg