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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATATCTTAGCCCACATGCATCAGGGAAAAACCTCCTTATTGGAGCAAACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttggaatgaataattaacatatggttttactttacaagaattctgattttaacaatttcttttattccttttttggcag

Basic information

species Glycine max
transcript GLYMA08G21340.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21340.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv09s0002g03140.t01 (Vitis vinifera), 5'ss of exon 2
AGCATATCTTAGCCCACATGCATCAGGGAAAAACCTCCTTATTGGAGCAAACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttggaatgaataattaac--atatggtttt--actttacaagaattctgattttaacaatttcttttattccttttttggcag--------------------------------------------------------------------------------------------
|||||| ||||||||  | ||||||||||| ||||| || |||||||| |||||||| || ||||  |||||||||||||| ||  | || |  || | ||||||     | |     |||  |   | |||||    |    |||| | |||  ||  | | |  || ||  | | |  |||   ||                                                                                             
AGCATACCTTAGCCCCAAGGCATCAGGGAAGAACCTTCTGATTGGAGCCAACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaaga--aaattcccccattctctagtttggttgccaagaaaacaaaatttccaatcatcaaacattgttccaatacactttcaacacacagagttttcatattagtattgtgatcgcaagataatcactcatatagtctcctctttctcggcatttttctacttcaaatcttgttgcag
















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|213588547|gb|DB957502.1|DB957502
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|13181281|gb|BG352621.1|BG352621
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|209703924|gb|BW667940.1|BW667940
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|209702092|gb|BW652332.1|BW652332
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTT
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTT
EST: gi|298172433|gb|HO019473.1|HO019473
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|209725337|gb|BW658235.1|BW658235
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|213599922|gb|DB966438.1|DB966438
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|208336984|gb|GE137628.1|GE137628
EST:     CTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: CTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|209721115|gb|BW666376.1|BW666376
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|151401815|gb|EV271628.1|EV271628
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|209727381|gb|BW651929.1|BW651929
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|298192370|gb|HO036452.1|HO036452
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAGGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|213588481|gb|DB961598.1|DB961598
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|9898887|gb|BE607855.1|BE607855
EST:     CTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: CTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|209728723|gb|BW655416.1|BW655416
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|192297806|gb|FG993145.1|FG993145
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCGAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|298176726|gb|HO026847.1|HO026847
EST:     TCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: TCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|213602242|gb|DB958502.1|DB958502
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|192310311|gb|FK002191.1|FK002191
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCGAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|192331456|gb|FK022732.1|FK022732
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|298182833|gb|HO031568.1|HO031568
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCAACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
EST: gi|298194944|gb|HO043416.1|HO043416
EST:     ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAAT                         CACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC
genomic: ACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttgg ... tttttggcagCACGCGATTCCGTTGTCCCAACAGTTGAGTTATTTCAAGGAATACCAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATATCTTAGCCCACATGCATCAGGGAAAAACCTCCTTATTGGAGCAAACTTTGCTTCAGCTGCATCTGGTTATGATGAAAATGCTGCTACTTTGAATgtaagtttggaatgaataattaacatatggttttactttacaagaattctgattttaacaatttcttttattccttttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT