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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattactgtttggttaatttttgtttgttgttaattgcatttgatgcttcatttgtatctaatttttttaatcttttaatgtttccccaacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGGCCAGTGCCAGTGATGAAAAGCAGACTTCAGATTCGAGAAGTGTCGTGGA

Basic information

species Glycine max
transcript GLYMA17G05530.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 8
--taaattactgtttg----gttaatttttgtttgttgttaattgcatttgatgcttcatttgtatctaatttttttaatcttttaatgtttccccaacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGGCCAGTGCCAGTGATGAAAAGCAGACTTCAGATTCGAGAAGTGTCGTGGA
  || | | ||         |  |||  |  |||  | ||||||||| |   ||| |       | |||   ||  | |||| |     ||| |     | | ||||||  ||||||||||| |||||||||||||||||||||||||| ||||| ||  | |  |  || || ||||  | ||||||| | | |||||| |||||
catagaatgcttcaaaagatgcaaatagtattttcctcttaattgcaatc--tgcatgtgggaaaactatgcttgcttatctgtcctgatttgca----attacagGAAGGTGGCTTGGAAGCAGACAGATTCGTTGTAATTGGGCAACAAAAGGTGCTGGAGGTAACGAGGACAAGCCAAATTCAGATGCCAAAAGTGTTGTGGA
















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|10709423|gb|BF009147.1|BF009147
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193439256|gb|FK406341.1|FK406341
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|207750871|gb|GD726126.1|GD726126
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|207753671|gb|GD723269.1|GD723269
EST:     GATGCCCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|15285660|gb|BI469551.1|BI469551
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|11687387|gb|BF595063.1|BF595063
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193490170|gb|FK455505.1|FK455505
EST:     TCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: TCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|207711809|gb|GD693189.1|GD693189
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|7925242|gb|AW831268.1|AW831268
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208150143|gb|GD950790.1|GD950790
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|207805431|gb|GD776877.1|GD776877
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208052705|gb|GD850028.1|GD850028
EST:     ATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: ATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193616957|gb|FK571627.1|FK571627
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208265654|gb|GE063182.1|GE063182
EST:     GATGCTCAAAGTGCTAT-AATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208049063|gb|GD846664.1|GD846664
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193680125|gb|FK620755.1|FK620755
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193430767|gb|FK394203.1|FK394203
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|5175311|gb|AI759644.1|AI759644
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193500769|gb|FK464566.1|FK464566
EST:     TCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: TCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|6454619|gb|AW185302.1|AW185302
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208092344|gb|GD889381.1|GD889381
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|21889247|gb|BQ742460.1|BQ742460
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|21637806|gb|BM107961.1|BM107961
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAARGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|193624299|gb|FK573395.1|FK573395
EST:     TCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: TCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208277576|gb|GE079567.1|GE079567
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTT
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTT
EST: gi|19053974|gb|BM732641.1|BM732641
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
EST: gi|208067943|gb|GD861453.1|GD861453
EST:     GATGCTCAAAGTGCTATAAATGATTTGACTG                         GAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG
genomic: GATGCTCAAAGTGCTATAAATGATTTGACTGgtaagataaa ... aacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttcatttgtatctaatttttttaatcttttaatgtttccccaacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGGCCAGTGCCAGTGATGAAAAGCAGACTTCAGATTCGAGAAGTGTCGTGGA
                              ttttaat  putative branch site (score: 3)
                                      tttcccca  CT-rich tract
     tcatttgtatctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattactgtttggttaatttttgtttgttgttaattgcatttgatgcttcatttgtatctaatttttttaatcttttaatgtttccccaacacttcagGAAAATGGCTTGGAAGTAGACAGATTCGTTGTAATTGGGCAACCAAAGGGGCCAGTGCCAGTGATGAAAAGCAGACTTCAGATTCGAGAAGTGTCGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT