Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacgtgtttaatgggaagaagagctttctattgtaagagctgcaaatgtttggagctcccattatgttgcatgacaatgccttaatttttgttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAAGCCAAGTATTGAGAGGGAGCCTGCGTTCAATGAGGTCAGATAACTTACA

Basic information

species Glycine max
transcript GLYMA20G31760.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31760.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g03670.t01 (Vitis vinifera), 3'ss of exon 11
-----gacgtgtttaatgggaagaagagctttctattgtaagagctgcaaatgtttggagctcccattatgttgcatgacaatgccttaatttttgttatgc--cagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAAGCCAAGTATTGAGAGGGAGCCTGCGTTCAATGAGGTCAGATAACTTACA
      ||   ||||    |   | |    ||   ||   | ||||  |   | |   |      || || ||   |   | ||| || || ||  || ||   |||| || |||||||||| |||||||||||||||||| | |||     ||  ||| |||| || || || || ||||| || ||||||               
cacttaactcttttatcctgctaaggcatgtt---ttcagaaagctagaccagctataaat----ataatatttattttaattgctttgatcttctttttggtgcagGCTGCAGAGAGATGCATTGCCTCTTTTTAATATGCTAAGACAGTCTTACAAGTCAAGCATAGATAGAGAACCTGCATTTAATGAG---------------
















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|208039762|gb|GD838490.1|GD838490
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATG
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATG
EST: gi|207733230|gb|GD710032.1|GD710032
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208270898|gb|GE066574.1|GE066574
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTTAATATGTTGAGAACAAATTTTA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTT-AATATGTTGAGAACAAATTTTA
EST: gi|208316022|gb|GE110990.1|GE110990
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTACTTTTTAAATAATGTTGAGAACAAATTT
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCT-CTTTTTAA-TA-TGTTGAGAACAAATTT
EST: gi|208271397|gb|GE072603.1|GE072603
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193332005|gb|FK299429.1|FK299429
EST:     GCGTTTCCTAAGACAAAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGAATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGA-TGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTA
EST: gi|193543207|gb|FK502470.1|FK502470
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTTCTTTTTAATATGTTGAGAACAAATTTTA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCT-CTTTTTAATATGTTGAGAACAAATTTTA
EST: gi|193697015|gb|FK635315.1|FK635315
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAAGAAGAATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTT
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGA-GA-GA-TGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTT
EST: gi|208132251|gb|GD930282.1|GD930282
EST:     CGTTTCCTAAGACAGAGTTGATGCAAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAGCAAATTTTAA
genomic: CGTTTCCTAAGACAGAGTTGATGCAA-TTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208080211|gb|GD878527.1|GD878527
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAGCAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208131226|gb|GD931113.1|GD931113
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208298185|gb|GE092406.1|GE092406
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193348660|gb|FK314852.1|FK314852
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208153520|gb|GD945739.1|GD945739
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|207716671|gb|GD698145.1|GD698145
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208317520|gb|GE116217.1|GE116217
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208150094|gb|GD951668.1|GD951668
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATTATGTTGAGAACAAATTT
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAAT-ATGTTGAGAACAAATTT
EST: gi|208158290|gb|GD956867.1|GD956867
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|207783116|gb|GD757137.1|GD757137
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAANATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193689259|gb|FK632646.1|FK632646
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|207829276|gb|GD798154.1|GD798154
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193654022|gb|FK597010.1|FK597010
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTCTGCCTCTTTTTTAATATGTTGAGAACAAATTTTA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTT-AATATGTTGAGAACAAATTTTA
EST: gi|193593608|gb|FK548002.1|FK548002
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAANATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208135113|gb|GD928832.1|GD928832
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAANATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193438722|gb|FK401019.1|FK401019
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTT-GCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|208112117|gb|GD914133.1|GD914133
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193602966|gb|FK559341.1|FK559341
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193526419|gb|FK486661.1|FK486661
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAA
EST: gi|193521777|gb|FK481230.1|FK481230
EST:     GTTTACCTAAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTCTTTTTTAATATGTTGAGAACAAATTTTA
genomic: GTTT-CCTAA-GACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTT-AATATGTTGAGAACAAATTTTA
EST: gi|193710399|gb|FK648655.1|FK648655
EST:     GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAAC                         GTTGGAGAGAGATGCTTTGCCTTCTTTTTAATATGTTGAGAACAAATTTTA
genomic: GCGTTTCCTAAGACAGAGTTGATGCAATTCATCACTTATCTTTTGCAAACgtaagttttc ... gttatgccagGTTGGAGAGAGATGCTTTGCCT-CTTTTTAATATGTTGAGAACAAATTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttggagctcccattatgttgcatgacaatgccttaatttttgttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAAGCCAAGTATTGAGAGGGAGCCTGCGTTCAATGAGGTCAGATAACTTACA
                                  ccttaat  putative branch site (score: 4)
                                        tttttgtt  CT-rich tract
                                    ttaatttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacgtgtttaatgggaagaagagctttctattgtaagagctgcaaatgtttggagctcccattatgttgcatgacaatgccttaatttttgttatgccagGTTGGAGAGAGATGCTTTGCCTCTTTTTAATATGTTGAGAACAAATTTTAAGCCAAGTATTGAGAGGGAGCCTGCGTTCAATGAGGTCAGATAACTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG