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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcttttgtgggtgtatgatcattgaatagtcaaaggttggattttttcttgtgtttgattggtttgtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTTAACCAGTTAGCTGAGCAGCTTCAGAGATCTGTGCCAACCGGATCTCATG

Basic information

species Arabidopsis thaliana
transcript AT2G17390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 3
--------gtaagttctcttttgtgggtgtatgatcattgaatagtcaaaggttggattttttcttgt----gtttgattggtttgtt------tattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTTAACCAGTTAGCTGAGCAGCTTCAGAGATCTGTGCCAACCGGATCTCATG
        || || | | |   || | ||  |  ||| |   || || |   |   |||| ||| | |    ||   | || ||   |      |    |||||||||||||||||||||||||||| || ||||| |||||||| ||||| |||||| | |||||||||||||||| | || | | |   |   | || |
ttttgtttgtcagatgtttggagttgttggctc-tcaatttctattctatattaatatttcttcatataggcgtactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCATTCAACCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAGG

upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 3
-------gtaagttctcttttgtgggtgtatgatcattgaatagtcaaaggttggattttttcttgtg----tttgattggtttgtt------tattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTTAACCAGTTAGCTGAGCAGCTTCAGAGATCTGTGCCAACCGGATCTCATG
       ||  ||    | ||  | ||      ||| |   || || |   |   |||| ||| | |     |   | || ||   |      |    |||||||||||||||||||||||||||| || ||||| |||||||| || || || ||| | |||||||||||||||| | || | | |   |   | || |
gaattttgtttgtcagatgtttggagttggctctcaatttctattctatattaatatttcttcatataggcatactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTCAATCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAAG
















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|86055531|gb|DR351288.1|DR351288
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|125231635|gb|EL245720.1|EL245720
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATC
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATC
EST: gi|86055530|gb|DR351287.1|DR351287
EST:     GGCTTGATTTCWATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCYAAGTATCAAGGAATTGGCTGAGCAAWTAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055524|gb|DR351281.1|DR351281
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|116476826|gb|EG519418.1|EG519418
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|164113894|gb|ES090872.1|ES090872
EST:     GGATTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATC
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATC
EST: gi|124965838|gb|EL039990.1|EL039990
EST:     GGCTTGATTTCAATGCCTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAAT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAAT
EST: gi|86055526|gb|DR351283.1|DR351283
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055536|gb|DR351293.1|DR351293
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055528|gb|DR351285.1|DR351285
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055533|gb|DR351290.1|DR351290
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055525|gb|DR351282.1|DR351282
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTVGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCATAAAGATCCTTCATT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGC-TAAAGATCCTTCATT
EST: gi|86055527|gb|DR351284.1|DR351284
EST:     GGATTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|124714538|gb|EH805940.1|EH805940
EST:     CTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAAGCTAAAGATCCTTCATT
genomic: CTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATA-GCTAAAGATCCTTCATT
EST: gi|86055532|gb|DR351289.1|DR351289
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|164089145|gb|ES136080.1|ES136080
EST:     GCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055534|gb|DR351291.1|DR351291
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055523|gb|DR351280.1|DR351280
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|116419184|gb|EG461776.1|EG461776
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
EST: gi|86055535|gb|DR351292.1|DR351292
EST:     GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT
genomic: GGCTTGATTTCAATGCTTTTGATTTCTCCGGCATGGCTGGGATCCTCAATgtaagttctc ... gtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaatagtcaaaggttggattttttcttgtgtttgattggtttgtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTTAACCAGTTAGCTGAGCAGCTTCAGAGATCTGTGCCAACCGGATCTCATG
                                gtttgat  putative branch site (score: 5)
                                          tttgttt  putative PPT
                    attttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctcttttgtgggtgtatgatcattgaatagtcaaaggttggattttttcttgtgtttgattggtttgtttattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTTAACCAGTTAGCTGAGCAGCTTCAGAGATCTGTGCCAACCGGATCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC