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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTCCGAAGAAACCTAATTGGGACCTTCGGAGAGACGTGCAGAAGAAGCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagcatctccttaatattccttatttctgttgttcgatgaattattcatcttattaatatctgttatatgctgaatggttatggctattttctc...

Basic information

species Glycine max
transcript GLYMA20G35890.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35890.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G05070.1 (Arabidopsis thaliana), 5'ss of exon 4
ATTGCTCCGAAGAAACCTAATTGGGACCTTCGGAGAGACGTGCAGAAGAAGCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagcatctccttaatattcct-tatttctgttgttcgatgaattattcatcttattaatatctgttatatgc-tgaatggttatggctattttctc
|| ||||| ||||| || || |||||||| || ||||| |||||||||||||||||||||||||| | ||| ||||| |||||  |  || ||||||||||||  |    |     |  | || |   ||| |    |||  | |  || ||| |    |||| | | || |   ||  | | ||  ||    |    |   
ATCGCTCCAAAGAAGCCAAACTGGGACCTCCGAAGAGATGTGCAGAAGAAGCTTGATAAGCTCGAAAGGCGGACTCAAAAGGCAATGCATAAACTCATGGgtaagtggcaactgtatctacatactgatatcttctatgtaagcttgataattaagac-attagtctgtggttcgtgagtaagtgagtaacatttcactga-

upper sequence: GLYMA20G35890.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv16s0039g00370.t01 (Vitis vinifera), 5'ss of exon 4
ATTGCTCCGAAGAAACCTAATTGGGACCTTCGGAGAGACGTGCAGAAGAAGCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc-atctccttaatattcctta---tttctgttgttcgatgaattattcatcttattaatatctgttatatgctg-aatggttatggctattttctc
|||||||| ||||| || || ||||||||||| || |||||||||||||||||||||||||| || |  || || || |||||  | | | |||| ||||||   |||   ||    ||  ||    ||    | ||  || | |  |||    || |   | |||  || ||||     |   ||||| |||     |      
ATTGCTCCAAAGAAGCCAAACTGGGACCTTCGAAGGGACGTGCAGAAGAAGCTTGATAAGCTTGAAAGACGTACACAAAAGGCAATATTTAAACTGATGGgtgagtaatttattgaattggtacctattgagttgtcaattttcctgtgag---tttaagctgttaggatttgtttgggcccataatggatatcatgctcaaa--
















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|298183405|gb|HO028618.1|HO028618
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|298197992|gb|HO039531.1|HO039531
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATA
EST: gi|298173124|gb|HO020108.1|HO020108
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATG
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATG
EST: gi|151407942|gb|EV277757.1|EV277757
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|298177951|gb|HO023800.1|HO023800
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|13252177|gb|BG363080.1|BG363080
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|208152867|gb|GD949608.1|GD949608
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAAT
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAAT
EST: gi|298181747|gb|HO025922.1|HO025922
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAGCTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|298188525|gb|HO035218.1|HO035218
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAG
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAG
EST: gi|207734655|gb|GD710702.1|GD710702
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|298175116|gb|HO014919.1|HO014919
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|207795453|gb|GD766380.1|GD766380
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|298182540|gb|HO031275.1|HO031275
EST:     GCTTGATAAGCTTGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|193550551|gb|FK508428.1|FK508428
EST:     GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
EST: gi|192328551|gb|FK023555.1|FK023555
EST:     GCTTGATAAGCTCGAGAGGCGAACTCAGAAGGCTCTCTATCAACTCATGG                         TGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA
genomic: GCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagc ... ctttttacagTGGAACAAGAGAAGCAAAATCAATTGACTGAAGGAGATGATACAAATGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTCCGAAGAAACCTAATTGGGACCTTCGGAGAGACGTGCAGAAGAAGCTTGATAAGCTCGAGAAGCGAACTCAGAAGGCTCTCTATCAACTCATGGgtatttaagcatctccttaatattccttatttctgttgttcgatgaattattcatcttattaatatctgttatatgctgaatggttatggctattttctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC