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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTTTCTCCTTCGCGCTTTGGTTCTCACAATGCTTTCCACTTACCACCTGGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttacttctaaccttgactatgcataactgaagtttcttgaattaccatggaagcatgacctatattatgattatctgtttggcag

Basic information

species Glycine max
transcript GLYMA04G09000.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09000.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv04s0008g03250.t01 (Vitis vinifera), 5'ss of exon 15
CACTTTCTCCTTCGCGCTTTGGTTCTCACAATGCTTTCCACTTACCACCTGGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttacttctaaccttgactatgc----ataactgaagtttcttgaattaccatggaagcatgacctatattatgattatctgtttggcag----------
|||| |||||||| || |||||  |||| |  | ||| | |  || ||| |||||||||||||| || ||||||||||| ||||||||| | |||||  ||   ||    || |  |||    ||||    || |   |    ||| ||  ||  ||      || | |||| ||    | ||      || |           
CACTCTCTCCTTCTCGATTTGGCCCTCAAATGGGTTTTCGCCCACTACCAGGCACTCCTGAGGCGCACACACTTGCTCGGTGGATCTGTCAGAGCTATAGgtgcgtag--tcaagtcttagtcatgcttctatcatctagagctctggacctag-atatttatat-atctatgtttcagtaatacaagagggacataacatata
















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|208186467|gb|GD983050.1|GD983050
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|208197450|gb|GD997173.1|GD997173
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|193362602|gb|FK325356.1|FK325356
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|208060371|gb|GD856223.1|GD856223
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|193356332|gb|FK323045.1|FK323045
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|26057413|gb|CA800327.1|CA800327
EST:     ACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: ACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|193356289|gb|FK320552.1|FK320552
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTTGAATCCATTC
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGT-GAATCCATTC
EST: gi|193518039|gb|FK476968.1|FK476968
EST:     CTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: CTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|208188940|gb|GD981874.1|GD981874
EST:     GGCACTCCCGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|208144355|gb|GD942106.1|GD942106
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|208269640|gb|GE071698.1|GE071698
EST:     CAAACACTTGCTCGATGGATCTGTAACAGCTATCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAGTCCATTCT
genomic: CAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|208314940|gb|GE115270.1|GE115270
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAAGGCAGTGAATCCATTCT
EST: gi|19452311|gb|BM953721.1|BM953721
EST:     GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCG                         GTTCTATCTTGGGGTAGAACTTCTAAAATGTGAA
genomic: GGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttact ... tgtttggcagGTTCTATCTTGGGGTAGAACTTCTAAAATGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTTTCTCCTTCGCGCTTTGGTTCTCACAATGCTTTCCACTTACCACCTGGCACTCCTGAGGCACAAACACTTGCTCGATGGATCTGTAACAGCTACCGgcatgttacttctaaccttgactatgcataactgaagtttcttgaattaccatggaagcatgacctatattatgattatctgtttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA