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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgtttctgggatttataattgttttagaaaaatgttatcagaatgttaattttttttttcctgtaaataaaatattttggaatgaattctgttacagcttttacttttcccccctaactgtattgtgttgattgtttttggtgatgttgtttcccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG

Basic information

species Glycine max
transcript GLYMA13G18950.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G20360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtatgtttctgggatttataattgttttagaaaaatgttatcagaatgttaattttttttttcctgtaaataaaatattttg-gaatgaattctgttacagcttttacttttcccccctaactgtattgtgttgattgtttttggtgatgttgtttcccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG
                                                   || | ||   ||| || |    || |    ||  |  ||| |||  ||||     ||||   |        | | | |||| ||||  ||| |      || ||   |    |   ||||||||||||||||| ||||| || ||||||||||||||||| || ||   ||| || |||||||| |||||||| ||||| ||||||
---------------------------------------------------gtgagttgggtttatcattggtattaccagttgggtaaatcaatcttgttttttattttg--tacatttgttgattttattttgttacttgctaaactcga-gtgaatcttttctactagCTAAAATGGGATCACAAGTGCTTGTTCCTTTCCGAGGCTCAGAGGACTCTCCTCGACATCTCAAGTTGATGGGAGATTTAGGACAG

upper sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtatgtatgtttctgggatttata-attgttttagaaaaatgtt--atcaga-atgttaattttttttttcctgtaaataaaatattt-tggaatgaattct---gttacagcttttactttt-----cccccctaactgtattgtgttgat-tgtttttggtgatgttgtttcccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG
                 | | |  || ||| | |   | ||||    |    | | ||  ||   | |||| | ||| | | | | | |   ||   ||    |||    | ||||    || ||   ||     |            |  || | ||    | ||   | |||| |  | || |     ||  | ||||||||||||||| |||||  | |||||||||||||| ||||| |||  ||  |||||||| ||||||||||| ||||| ||||||
gtgagtggaatataaattttgttattatggaactagcacattggcccatgttatttttgtattgtatatgtgattttgtatctgcatatttctatcgtaaacgtggggaaagttctctaattccaagcttggtggtggaaagtttttgtttctatttttctctaatacatgtttgcttgtattataattttttcccagCTAAAATGGGATCCCAAGTGTTGGTTCCTTTCCGAGGTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG
















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|209703775|gb|BW670711.1|BW670711
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|151400304|gb|EV270118.1|EV270118
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|298181570|gb|HO025745.1|HO025745
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|192301726|gb|FG997640.1|FG997640
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|298190384|gb|HO032505.1|HO032505
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAACGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGGAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|151398563|gb|EV268434.1|EV268434
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|298192730|gb|HO033164.1|HO033164
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|151403355|gb|EV273165.1|EV273165
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|209718615|gb|BW662707.1|BW662707
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|254347887|gb|GR854136.1|GR854136
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|213595497|gb|DB966551.1|DB966551
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|192312569|gb|FK005027.1|FK005027
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGA-GAATAAT
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGA-TAAT
EST: gi|213591304|gb|DB959874.1|DB959874
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|151397287|gb|EV267160.1|EV267160
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|298184881|gb|HO030094.1|HO030094
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|209707137|gb|BW656754.1|BW656754
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|12774559|gb|BG239486.1|BG239486
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCA-CAACTTG                         CTAAA-TGG-ATCTCAGGTC-TAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|14258415|gb|BG881323.1|BG881323
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|209709595|gb|BW661922.1|BW661922
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|209714364|gb|BW677064.1|BW677064
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|298174324|gb|HO017660.1|HO017660
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
EST: gi|192312568|gb|FK005026.1|FK005026
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGA-GAATAAT
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGA-TAAT
EST: gi|192300056|gb|FG991860.1|FG991860
EST:     AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTG                         CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC
genomic: AGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgtatgt ... ccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccccctaactgtattgtgttgattgtttttggtgatgttgtttcccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG
                                      ttgtttcccttgtct  CT-rich tract
                      attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatgtttctgggatttataattgttttagaaaaatgttatcagaatgttaattttttttttcctgtaaataaaatattttggaatgaattctgttacagcttttacttttcccccctaactgtattgtgttgattgtttttggtgatgttgtttcccttgtctagCTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA