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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtcatcttgaaattgaacttactattatatacgtaatcagttttacattattgattgttggtttgctcattaatctggcctggctgaacaaaag

Basic information

species Glycine max
transcript GLYMA04G42670.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42670.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ25898 (Selaginella moellendorffii), 5'ss of exon 9
GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtg--tcatcttgaaattgaacttactattatatacgtaatcagttttacattattgattgttggtttgctcattaatctggcctggctgaacaaaag
|||||||||  | || ||||||||||| ||||| ||  | |||||||| ||||| |||||||| ||||||||||| |    || ||||    |  ||||   |     |  |         |  | |  |                                            
GTATGCAAGCGCGTTCTATGGTCCATTCAGAGAAGCTTTGGACTCAAATCCCCGTTTTGGAGATAAGAAAACgtaagcagttcctctttttctccaactcttttgctcactctctggagaatgaaaaccag-------------------------------------------

upper sequence: GLYMA04G42670.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ10919 (Selaginella moellendorffii), 5'ss of exon 9
GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtg--tcatcttgaaattgaacttactattatatacgtaatcagttttacattattgattgttggtttgctcattaatctggcctggctgaacaaaag
|||||||||  | || ||||||||||| ||||| || || |||||||| ||||| |||||||| ||||||||||| |    || |||| |  |  ||||   |     |  |         |  | |  |                                            
GTATGCAAGCGCGTTCTATGGTCCATTCAGAGAAGCTCTGGACTCAAATCCCCGTTTTGGAGATAAGAAAACgtaagcagttcctctttatctccaactcttttgctcactctctggagaatgaaaaccag-------------------------------------------
















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|7028233|gb|AW458016.1|AW458016
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|7691223|gb|AW759354.1|AW759354
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|6455519|gb|AW186202.1|AW186202
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|208060750|gb|GD856686.1|GD856686
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTCTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|23057473|gb|BU578156.1|BU578156
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|208339448|gb|GE138566.1|GE138566
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|17022525|gb|BM093559.1|BM093559
EST:     CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGAGATGCGGGA
EST: gi|7693203|gb|AW761299.1|AW761299
EST:     CCATTTAGAGAGGCACTAGACTCAGACCCGCGGTTTGGAGACAAGAAAAC                         TTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTGNAGATGCGG-
genomic: CCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtca ... tgaacaaaagTTATCAGATGAACCCAGCTAATTACAGAGAGGCTCTGACTG-AGATGCGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAACgtatgtgtcatcttgaaattgaacttactattatatacgtaatcagttttacattattgattgttggtttgctcattaatctggcctggctgaacaaaag

- - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA