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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttcattgggttgtgaaatttctgtgtaattgtattttggagaagatattgatttggttaggtattaatcaatctatatttctctgttattggtttagGTTTGTGAAGGTTTTTTCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGGAAGAGTGCGTATGCCCGCAAACAATCGGGTGCATAGTAGTGCAGCGCTTC

Basic information

species Arabidopsis thaliana
transcript AT2G28910.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G23830.1 (Glycine max), 3'ss of exon 1
----aatttcattgggttg----tgaaatttctgtgtaattgtattttggagaagatattgatttggttaggtattaatcaatctatatttctctgttattggtttagGTTTGTGAAGGTTTTTTCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGGAAGAGTGCGTATGCCCGCAAACAATCGGGTGCATAGTAGTGCAGCGCTTC------
       || | ||||       |  ||| | |   |  || | ||||    |||   ||| ||  |||    ||   | | | | | ||||||| |    |||   || ||  |||         |      ||   |||||||| || ||||||||||| || |||||||| || |||||| |||| || || |||||||||||||      
acattcctttactgggaaagagatagaatcttttcttgcttctgttttttttaagcc-ttgtttcagttcctgatggttaagtttctttttctct-tcgcagGTGAGGGATT-CGAA--------TTGAAACCTC---AAGATGCCAGCCACAGCAGGAAGGGTTCGTATGCCTGCGAACAATAGGGTTCACAGCAGTGCAGCGCTTCAAACCC

upper sequence: AT2G28910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G43090.1 (Glycine max), 3'ss of exon 1
-------aatttcattgggtt----gtgaaatttctgtgtaattgtattttggagaagatattgatttggttaggtattaatcaatctatatttctctgttattggtttagGTTTGTGAAGGTTTTTTCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGGAAGAGTGCGTATGCCCGCAAACAATCGGGTGCATAGTAGTGCAGCGCTTC------
         ||||| ||||         |||| | | | |  || ||||||   |      ||| ||  |||   |  |  | ||  |  ||||     ||   |||   || |||  |  |  |  ||            |||||||| || ||||||||||| || || ||||| || |||||| |||| || || |||||||||||||      
gttatattctttcactgggaaagagagaaaatctttttttgcttatatttttttg----ccttgtttcagttcc-tgatggttaagttgcattttctctttgcagGTGAGGGATTGAAATTGAATCCTC------------AAGATGCCAGCTACAGCAGGAAGGGTTCGCATGCCTGCGAACAATAGGGTTCACAGCAGTGCAGCGCTTCAAACCC

upper sequence: AT2G28910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S62_131V6.1 (Physcomitrella patens), 3'ss of exon 1
-aatttcattgggttgtgaaatttctgtgtaattgtattttggagaagatattgatttggttaggtattaatcaatctatatttctctgttattggtttagGTTTGTGAAGGTTTTTTC--TAGGGTTTCGAAAA------GATGCCGGCGACAGCAGGAAGAGTGCGTATGCCCGCAAACAATCGGGTGCATAGTAGTGCAGCGCTTC
    | ||   |  |  |  |   | ||||     ||   | |      |||   || | |    | |  |   ||  ||  |    || |  ||    |||||   |||  ||||  |  |   || | |||||      ||||||||| || |||||  ||||||| ||||||||||||||||||||||||   |||||        
gtgctacaccagcgttggccacggcagtgtc-cactaacctagcaccactatcttttcgatggtttttacaaggattgatcctgaaatggtggtgcagcagGTTGCAGAACTTTTTAGCAGTTAAGTCTTGAAAACAGCAAGATGCCGGCCACGGCAGGCCGAGTGCGCATGCCCGCAAACAATCGGGTGCATTCGAGTGC--------

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|116475246|gb|EG517838.1|EG517838
EST:     ATCCATCTCTCTCCGTCGCTTCTTCCTAACGATTCCTTCACTCGAATCAG                         GTTTGTGAAGGNNNNNNNCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGG
genomic: ATCCATCTCTCTCCGTCGCTTCTTCCTAACGATTCCTTCACTCGAATCAGgtaaactatt ... attggtttagGTTTGTGAAGG-TTTTTTCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGG
EST: gi|164213387|gb|ES016710.1|ES016710
EST:     ATCCATCTCTCTCCGTCGCTTCTTCCTAACGATTCCTTCACTCGAATCAG                         GTTTGTGAAGGTTTTT-CTAGGGTTTCGAAAAGATGCCG
genomic: ATCCATCTCTCTCCGTCGCTTCTTCCTAACGATTCCTTCACTCGAATCAGgtaaactatt ... attggtttagGTTTGTGAAGGTTTTTTCTAGGGTTTCGAAAAGATGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatattgatttggttaggtattaatcaatctatatttctctgttattggtttagGTTTGTGAAGGTTTTTTCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGGAAGAGTGCGTATGCCCGCAAACAATCGGGTGCATAGTAGTGCAGCGCTTC
                   tattaat  putative branch site (score: 2)
                   tattaatcaatctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttcattgggttgtgaaatttctgtgtaattgtattttggagaagatattgatttggttaggtattaatcaatctatatttctctgttattggtttagGTTTGTGAAGGTTTTTTCTAGGGTTTCGAAAAGATGCCGGCGACAGCAGGAAGAGTGCGTATGCCCGCAAACAATCGGGTGCATAGTAGTGCAGCGCTTC

- - - - - - - - - - - - - - - - - -attttgg
- - - - - - - - - - - - - - - - - - - - - -gaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - gatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taatcaa