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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtactataattgccatgtgattttgatttgttttgaagtttgaacagcatgctgatatacactcttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAAACTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCA

Basic information

species Glycine max
transcript GLYMA05G30140.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30140.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------------------------tttgtactataattgc--catgtgattttgatttgttttgaagtttgaacagcatgct-gatatacactcttgtggaat--ttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAAACTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCA
                                                        || |  ||    |||  ||| | | |  || || |||      ||   |   ||||  | | ||   |  | |   ||  | | |  |||||||  |||  |||||||| ||||||||||||||||| | ||||||||||||||| |||||||||||||| | ||| || |||||||| |||||||| || ||||||||   ||
gtatgtgatatactgtgtctgtctctcagtgtttaaaactgtcctatttattaaacttatcttacttctgctccattttaatgggaattttttcatttattatgcttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA
















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|120533277|gb|EH261410.1|EH261410
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTTAGTGCCAT                         GTAGAATTTTGATGAGGA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTT-GATGAGGA
EST: gi|208095648|gb|GD897138.1|GD897138
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGA
EST: gi|207819023|gb|GD790399.1|GD790399
EST:     AATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
genomic: AATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
EST: gi|207752054|gb|GD724495.1|GD724495
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGA
EST: gi|192313374|gb|FK005146.1|FK005146
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
EST: gi|193656048|gb|FK606678.1|FK606678
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
EST: gi|19347279|gb|BM892159.1|BM892159
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAA
EST: gi|6915949|gb|AW397479.1|AW397479
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
EST: gi|193531593|gb|FK490965.1|FK490965
EST:     TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAAGGAAA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAA-GGAAA
EST: gi|208156728|gb|GD957262.1|GD957262
EST:     TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGAACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
EST: gi|208226200|gb|GE025527.1|GE025527
EST:     ACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA
genomic: ACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagcatgctgatatacactcttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAAACTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCA
       tgctgat  putative branch site (score: 3)
                              tttttattttttgctt  putative PPT
                            aatttttattttttgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtactataattgccatgtgattttgatttgttttgaagtttgaacagcatgctgatatacactcttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAAACTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG