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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaactttcttgctctgttttcttgaatatctaaaaaaagtttctttgcccaaattatattttccaatatcacaatttattaatacaaggattattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG

Basic information

species Glycine max
transcript GLYMA13G27810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgaactttcttgctctgttttcttgaatatctaaaaaaagtttctttgcccaaattatattttccaatatcacaatttattaatacaaggattattcaac--agGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG
        |  || |  |||  ||  | || ||     |   | | |     |  | ||  ||   ||||| |    ||||  ||    | | |||| |    ||||||||||||||| ||||||||||||||  | ||| | ||||| || ||||  || ||   ||||||||||
-------gtaatgttg-gttcactctagtacctcctttacactccat-atttagctaatgcttctgaatattagggcttat--atgatggaactatttattttagGTCCTGCACTTGTATTTGAAGGAGAGGAATCTATGTTGGCTGCTATATCAGCAGACCCAATGAGTTTTAAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------gtgaactttcttgctctgttttc----ttgaatatctaaaaaaagtttctttgcccaaa---ttatattttccaatatcacaatttattaatacaaggattattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG
                             |  | |||| ||     |  |     |||     ||      |||||  | ||  |||   ||||    |  || |  | |  | |||  |  |||  || |||| ||||||||||||||||||||||||| ||||| || |||||||| || ||  ||||| |||||  ||| ||||||
gttctgttctatgtgctattttgtgttattataatttcctgaatcatactggaagttgctcgactccttgtagttttatagcttaaaattttatgcactgtaacaa-agagatgattgttcaaagacttgttcaccagGTCCTGCACTTGTCTTTGAAGGTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAG
















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|207741614|gb|GD717708.1|GD717708
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|207826331|gb|GD799442.1|GD799442
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTG
EST: gi|23734787|gb|BU765638.1|BU765638
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|193477699|gb|FK442288.1|FK442288
EST:     GGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: GGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|207820136|gb|GD790014.1|GD790014
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|208038473|gb|GD833239.1|GD833239
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|208154419|gb|GD952686.1|GD952686
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|151400516|gb|EV270330.1|EV270330
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|208287754|gb|GE081765.1|GE081765
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|16281629|gb|BI944586.1|BI944586
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|24136426|gb|BU926936.1|BU926936
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|208141207|gb|GD938251.1|GD938251
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
EST: gi|207822724|gb|GD793959.1|GD793959
EST:     ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTG                         GTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG
genomic: ACAGGGTTCCGTTGCTAAAATTACTGGAAAAGAAGGGCTGTACTTCTCTGgtgaactttc ... tattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccaaattatattttccaatatcacaatttattaatacaaggattattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG
                              tattaat  putative branch site (score: 2)
     aattatattttccaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaactttcttgctctgttttcttgaatatctaaaaaaagtttctttgcccaaattatattttccaatatcacaatttattaatacaaggattattcaacagGTCCTGCACTTGTCTTTGAAGGAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT