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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttctgcatagttcagatttcttgttgcaatgttttcttattagttatccatggctgatttttattgattcattttaggccatcttatttattg...

Basic information

species Glycine max
transcript GLYMA17G04720.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04720.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 2
TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttctgcat---agttcagatttcttgttg--caatgt-tttcttattagttatccatg-gctgatttttattgatt-------cattttaggccatcttatttattg-----------------
|||||||| | ||||| |||||  ||||||| ||| | || |||||||||||||||||||||| |  | |   ||   |  | |      |  |||  |||||  | |  |||  ||    |||  | |  ||| |  |||||         ||  |  |   |||||||| |                  
TTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAGgtattattaccagatttgatcttatggacatgattgaccaatgaatattatatatgtccaacatctgttattttctgctgattggaggactgttaaacactcacttatttaatctttgatgcattaaacag

upper sequence: GLYMA17G04720.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 5'ss of exon 1
----------------------------------------TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaa-----------tgcttctgcat-agt----tcagattt-cttgttgcaatgttttc-ttattagttatccatggctgatttttattgattcattttaggccatcttatttattg------------------------
                                        |||||||  | |||||||||||  ||||||| ||| |||| ||||||||||| || ||||||||           ||||||||||| |||    |||| ||    ||  ||   | ||||  | || |       |||     |||||  |  |      ||  |  |||| |  |                          
AATATGTAAAATAAGCTAAAATAAGTTACTTTTCCTGTAGTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag

upper sequence: GLYMA17G04720.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os07g14150.4 (Oryza sativa), 5'ss of exon 2
TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaa-----------tgcttctgcat-agt----tcagatttct-tgttgcaatgttttc-ttattagttatccatggctgatttttattgattcattttaggccatcttatttattg------------------------
|||||||  | |||||||||||  ||||||| ||| |||| ||||||||||| || ||||||||           ||||||||||| |||    |||| ||  | ||  ||   | ||||  | || |       |||     |||||  |  |      ||  |  |||| |  |                          
TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGgtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacag

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|298176038|gb|HO015443.1|HO015443
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|192328192|gb|FK020439.1|FK020439
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|16347143|gb|BI972738.1|BI972738
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|16347848|gb|BI973443.1|BI973443
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|5752974|gb|AI960261.1|AI960261
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTTCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|6964020|gb|AW432713.1|AW432713
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|14126393|gb|BG790831.1|BG790831
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|16347119|gb|BI972714.1|BI972714
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAACAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|21888734|gb|BQ741947.1|BQ741947
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|209723270|gb|BW651277.1|BW651277
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|151400238|gb|EV270052.1|EV270052
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|10846005|gb|BF068998.1|BF068998
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|14990698|gb|BI316371.1|BI316371
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|151407408|gb|EV277223.1|EV277223
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|120532313|gb|EH260446.1|EH260446
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|21888733|gb|BQ741946.1|BQ741946
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAATAATCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
EST: gi|14990622|gb|BI316295.1|BI316295
EST:     TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAG                         CCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT
genomic: TAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttc ... gcttaatcagCCGTGCAGGATAGAGACCACAAATTTTTAAGAAAAGCTGTTGAAGAAGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCATCAGGAAGgtaatgcttctgcatagttcagatttcttgttgcaatgttttcttattagttatccatggctgatttttattgattcattttaggccatcttatttattg

- - - - - - AGGATG
- - - - - - - GATGGA
- - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - TGCTGC