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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaatgcttgtcacttgtcagtgagcttgcatcaagaaatgcaacacacttcatgttagaaatgcaatctcatctgatcgggttcttcttgttttgccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT

Basic information

species Glycine max
transcript GLYMA17G07380.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ07726 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaaatgcttgtcacttgtcagtgagcttgcatcaagaaatgcaacacacttcatgttagaaatgcaatctcatctgatcgggttcttcttgttttgccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
                                             | ||  ||||  |    | | |||     ||  |||| ||      || | |||||| | |   ||||||| ||||| || |||||||||||||||||||| ||| |
---------------------------------------------gtaagtcactcaa----aaacatgtttcttcgcctgaccg----tatcatcttttgcttgt---agGGAGGTCTTGCTCCTGGTGGATTCAACTTCGATGCCAAACT

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ07670 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaaatgcttgtcacttgtcagtgagcttgcatcaagaaatgcaacacacttcatgttagaaatgcaatctcatctgatcgggttcttcttgttttgccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
                                                           || ||  |  |||   ||| |  |  |  |   | | | ||   | ||  ||||||| ||||| || |||||||||||||||||||| ||| |
-----------------------------------------------------------gtaagccactcaaaaacatttttttcgcctgaccgtatctt--ttgttgtagGGAGGCCTTGCTCCTGGTGGATTCAACTTCGATGCCAAACT
















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|6725436|gb|AW309835.1|AW309835
EST:     TTGTAGATA-TCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|151410382|gb|EV280197.1|EV280197
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|298173204|gb|HO020188.1|HO020188
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|18693005|gb|BM521853.1|BM521853
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|21887322|gb|BQ740535.1|BQ740535
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|151407803|gb|EV277618.1|EV277618
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|5175496|gb|AI759829.1|AI759829
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTAGCACCCAGTGGATTCAACTTCGATGCGATATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|51335738|gb|CO979604.1|CO979604
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|10235983|gb|BE804871.1|BE804871
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAAGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|22525640|gb|BU084451.1|BU084451
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|19934808|gb|BQ079838.1|BQ079838
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|5760217|gb|AI965580.1|AI965580
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|163921552|gb|EH039311.1|EH039311
EST:     TTGCAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|192327522|gb|FK018198.1|FK018198
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|298193926|gb|HO040574.1|HO040574
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|22932991|gb|BU550130.1|BU550130
EST:     NNNTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
EST: gi|13478586|gb|BG508003.1|BG508003
EST:     TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAAT                         GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
genomic: TTGTAGATATTCAAGAGGCGACACTGATTATGCTCAGTGTGATCAGAAATgtaagaaaat ... ccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttagaaatgcaatctcatctgatcgggttcttcttgttttgccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT
                    atctgat  putative branch site (score: 4)
                               ttcttcttgttttgcc  putative PPT
     tagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaatgcttgtcacttgtcagtgagcttgcatcaagaaatgcaacacacttcatgttagaaatgcaatctcatctgatcgggttcttcttgttttgccttttccagGGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA