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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG

Basic information

species Arabidopsis thaliana
transcript AT3G25230.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 2
gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG
                                                                      ||  |||   | ||  ||||  | ||||     |  ||  ||  |  | |   ||    | || |  ||  |  |  || |   | |  ||||||| | ||        |||| ||||| |||||||||||||||   |||||||| || ||||||||||||||||| ||| ||||||| || ||| | |||||||| ||||| ||||||||
----------------------------------------------------------------------tagattgtatgcta--aact--agttgaagggaaaatggcgtggaagtaatcttcaggctattttcaatataactcaaaagtgatatctttgttggaagtg--------cagGGCAAGTAATTAAAGGATGGGATGAAGGTATTAAAACCATGAAGAAAGGTGAAAATGCTATTTTCACCATCCCTCCCGAGCTAGCTTATGGTGAATCTGG

upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G32830.1 (Glycine max), 3'ss of exon 2
gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG-
                                                                       || |||    ||   ||  |   |  ||  | | | | |||  |  | |   ||    | || ||||  |      || |   |    ||||||| | ||        |||| ||||| |||||||||||||||   |||||||| || ||||||||||||||||| ||| ||||||| || ||| | |||||||| ||||| |||||||| 
-----------------------------------------------------------------------aaattgt---atgctaaactagttgaagggaaaatgggtgtggaagtaatcttcaggctatt-ttgagtataactcaaagtgatacctttgttggaagtg--------caggGCAAGTAATTAAAGGATGGGATGAAGGTATTAAAACCATGAAGAAAGGTGAAAATGCTATTTTCACCATCCCTCCCGAGCTAGCTTATGGTGAATCTGGT

upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G10730.1 (Glycine max), 3'ss of exon 2
gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG
                                                                           || | | |     |||   ||| |  | |   | | ||| |||   | | ||| |||||     |||  |   ||| ||||  ||   |||     ||    |||||| |||||||||||||||||||||   |||||||  || ||||||||||||||||| ||  ||||||| || || || |||||||| ||||| ||||||||
--------------------------------------------------------------------------atgtttgtttactcctttgtttgtggaacaa--ggtattacgttttga-ttgaaattttg-----gaacatactatgttttgacgtaagtggtgccctggaaatgcagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACAATGAAGAAAGGTGAAAATGCCCTTTTCACCATCCCAGCTGAGCTAGCTTATGGTGAATCTGG

upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 2
gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG
                                                                  |   |  |||  |   |||    |||||   || | || | ||||           || |||  ||||     ||||||   ||| ||||  ||   ||||    ||    |||||| |||||||||||||||||||||   |||||||  ||||||||||||||||||||  |  ||||||| || || || |||||||| ||||| ||| ||||
----------------------------------------------------------------acatgtttgtttattccttattttgttgaac-aaggtgtaat-gttg-----------attgaaaatttg-----gaatgtactatgttttgatgtaagtggcgccttggaaatgcagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACGATGAAGAAAGGTGAAAATTCCCTTTTCACCATCCCGGCTGAGCTAGCTTATGGTGAAACTGG

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|86070352|gb|DR366109.1|DR366109
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGG
EST: gi|301501375|gb|HO206915.1|HO206915
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
EST: gi|116475203|gb|EG517795.1|EG517795
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
EST: gi|116434999|gb|EG477591.1|EG477591
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
EST: gi|116475202|gb|EG517794.1|EG517794
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
EST: gi|116435001|gb|EG477593.1|EG477593
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
EST: gi|86070354|gb|DR366111.1|DR366111
EST:     TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG                         GTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG
genomic: TGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAGgtttgtgatt ... gtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG
     tgttgat  putative branch site (score: 4)
                                            tgttttt  putative PPT
                                            tgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT