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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctaagttagatttttgtcattattttgctttatcgcgtcacacaataatacttgctttactgaactccaaatatgtgccctaaaattgtgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATCCCTGCTCCTCCTAACGCTGCTGCTGCCTCTCCAACCTTGTCCATACATA

Basic information

species Glycine max
transcript GLYMA07G40240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40240.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G02570.3 (Arabidopsis thaliana), 3'ss of exon 2
------ttctaagttagatttttgtcattattt--tgctttatcgcgtcacacaataatacttgctttactgaactccaaatatgtgccctaaaattgtgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATCCCTGCTCCTCCTAACGCTGCTGCTGCCTCTCCAACCTTGTCCATACATA
          |||||  | || ||  | | |||  || | ||| | ||   |     | |  | ||  | |   |||  ||  | ||        |||    | | |||| ||||| ||||| |||||| | ||||||||||||||||| ||||| ||  ||    |   |  ||  | |  |||     ||||      |  ||   
ttgatccctgaagttctacttctgaaaatctttactgatatattgtgtataattgctagaaatcctcaatt---ctctgaaactttgttt-----ttgcaccatatagGTGATTGCATTGACAGAGGAAGTTCTTGCAACTGCAAAGCAAAATGAGATTTCTCTATCAGATGCCGGAGTTAGTGCTGAAGCAACTCCTGGCTCACCCG
















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|298191400|gb|HO038879.1|HO038879
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|298168743|gb|HO009673.1|HO009673
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|8669105|gb|BE190212.1|BE190212
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|298172500|gb|HO019540.1|HO019540
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|9820674|gb|BE556184.1|BE556184
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|21675141|gb|BQ627501.1|BQ627501
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|151393165|gb|EV263040.1|EV263040
EST:     ATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|37995015|gb|CF806604.1|CF806604
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|192331101|gb|FK020321.1|FK020321
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAGTC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|9564643|gb|BE474152.1|BE474152
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
EST: gi|192334366|gb|FK025543.1|FK025543
EST:     ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAG                         GTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC
genomic: ATGACCCTTCAAATTCTGAATATGCTGACATGGAGAGGGAACTTTCCGAGgtaagcttaa ... tgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatacttgctttactgaactccaaatatgtgccctaaaattgtgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATCCCTGCTCCTCCTAACGCTGCTGCTGCCTCTCCAACCTTGTCCATACATA
                                  ccctaaa  putative branch site (score: 3)
                                     taaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaagttagatttttgtcattattttgctttatcgcgtcacacaataatacttgctttactgaactccaaatatgtgccctaaaattgtgttacacagGTCATTGCTTTGACTGAGGAACTCCTTGCAACTGCAAAGCAGAATGAAATCCCTGCTCCTCCTAACGCTGCTGCTGCCTCTCCAACCTTGTCCATACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC