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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaagtcttgtgctaaccacagccatatattctcttgttagggcttcattttgggatgtggaaggaagaaaatgatgctggtttaaggttgtttaaatttatcaagatgcttttctaggttgattaatcattgttttgttgtggaaatatgcgtttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCACAGGAAGACAATCCTGCTAGAAAGGAATACATTAAGGGCCTGACTGAGA

Basic information

species Glycine max
transcript GLYMA20G28850.1
intron # 3
splice site 3'
intron type U2

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|209700828|gb|BW661259.1|BW661259
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|209710775|gb|BW676598.1|BW676598
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|214006646|gb|DB986397.1|DB986397
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|213617546|gb|DB969258.1|DB969258
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|213603188|gb|DB960451.1|DB960451
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|209727438|gb|BW669865.1|BW669865
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|151402210|gb|EV272023.1|EV272023
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|209727439|gb|BW669866.1|BW669866
EST:     CCCTAGACCCAAGTAACTATGTGAAG                         T
genomic: CCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcag-
EST: gi|209727439|gb|BW669866.1|BW669866
EST:     CCCTAGACCCAAGTAACTATGTGAAG                         T
genomic: CCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcag-
EST: gi|213607501|gb|DB978438.1|DB978438
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|209704143|gb|BW664761.1|BW664761
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|209704144|gb|BW664762.1|BW664762
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|192312775|gb|FK003987.1|FK003987
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|209710776|gb|BW676599.1|BW676599
EST:     CCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
EST: gi|192312776|gb|FK003988.1|FK003988
EST:     CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAG                         TTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA
genomic: CCGCTGGAATCTATCATCGCTTCACCCTAGACCCAAGTAACTATGTGAAGgtatgaaagt ... ttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctaggttgattaatcattgttttgttgtggaaatatgcgtttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCACAGGAAGACAATCCTGCTAGAAAGGAATACATTAAGGGCCTGACTGAGA
            gattaat  putative branch site (score: 3)
             attaatcattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaagtcttgtgctaaccacagccatatattctcttgttagggcttcattttgggatgtggaaggaagaaaatgatgctggtttaaggttgtttaaatttatcaagatgcttttctaggttgattaatcattgttttgttgtggaaatatgcgtttgtgtgcagTTAATGAGGTTGTTTAAGGGCGAGCCAGTGTGGACAGCATATAATCGACCACAGGAAGACAATCCTGCTAGAAAGGAATACATTAAGGGCCTGACTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA