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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtccactcttatgatttcaaatgttttgctctatttttatggtcttttatcgtgctgcatgtgaattttctcttttaatacttgcaatatttgatctaattgaaccttccaatcaaagactgaacaaactctattcttaatttcag

Basic information

species Glycine max
transcript GLYMA13G39270.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 4
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
AGCTGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtccactcttatgatttcaaatgttttgctctatttttatg-gtcttttatcgtgctgcatgtgaattttctcttttaatacttgcaatatttgatctaattgaaccttccaatcaaagactgaacaaactctattcttaatttcag
 ||||| || ||| ||  ||||||||| ||||| ||||| |||||||| ||  |||||||||||||||| || ||| |  |||| || || ||||| || ||  |||  | || |      | |  ||  | | | ||| | |  ||   | | | |   |     |  ||| || |  |||| | | |                                                                 
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaa-caacaccc----tcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag---------------------------------------------------------------

upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 8
AGCTGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtccactcttatgatttcaaatgttttgctctatttttatggtcttttatcgtgctgcatgtgaattttctcttttaatacttgcaatatttgatctaattgaaccttccaatcaaagactgaacaaactctattcttaatttcag
 |||||||| ||    || |||||||| ||||| ||||| |||||||| |||||||| ||||| ||||||||||| ||| |||| ||||| ||||| || ||| || |    | ||||    |   | | | | |  |||     || |  | | ||   | |  || | ||   ||||  | | | |||    ||  | |                                                    
TGCTGTGGGTAACTGCAGTATGGAGGAGAAGCAGATCTTTCAAAATGTGCAACTGAGCGTTAATTTCCTTGTCTCCTTGTTGAAGAAGAACTGGCAAAATgtgagttgatt-cacttagctctgttagtttatggaactaaaccaataggttatgataaagtt-tatattaaggctctcaatcagt-ctttaggtacctcact--------------------------------------------------

upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 3
AGCTGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggta-gtccactcttatgatttcaaatgttttgctctatttttatggtcttttatcgtgctgcatgtgaattttctcttttaatacttgcaatatttgatctaa-ttgaaccttccaatcaaagactgaacaaactctattcttaatttcag
 ||  | || ||   |   ||||||||||||||||||||||| ||   |||| || ||||||||||||| || ||  || |||| ||||| |||||||| ||  |||  |    || | |   ||  ||     |||  ||| | |   |  | || | ||| ||| ||| | |||  |  || | |  | |  |||     ||||| || |   ||  |   || |  ||||     | | |            
CGCCATCGGTAACTGTGATATGGAGGAAAAGCAAATCTTCCAGAACACACAAATGGGTGTTAACTTCCTCGTGTCCCTGTTGAAGAAGAACTGGCAGAATgtaagtacatttgttcctttctatttgaa-----tgcagtatatctgaagg-tgttcttgtgatgcttgt-attttcattattaagtgatggtcatacaatgtctaagttcagtattttatctaacgtttgaat---ttttgtaacag-------

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|208121079|gb|GD917066.1|GD917066
EST:     AAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|151407724|gb|EV277539.1|EV277539
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|193403245|gb|FK369443.1|FK369443
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|193514030|gb|FK468736.1|FK468736
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|213592002|gb|DB975208.1|DB975208
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|193698066|gb|FK640663.1|FK640663
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGA-TTGGCAGAAC                         GTTCGCTGCCTA
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTA
EST: gi|192308674|gb|FG999741.1|FG999741
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATTTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|193629110|gb|FK578058.1|FK578058
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
EST: gi|213588132|gb|DB979210.1|DB979210
EST:     AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAAC                         GTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT
genomic: AACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtc ... ttaatttcagGTTCGCTGCCTATATCTGAAGAGTACCATGGGGAAATCGTACCGTGTCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtccactcttatgatttcaaatgttttgctctatttttatggtcttttatcgtgctgcatgtgaattttctcttttaatacttgcaatatttgatctaattgaaccttccaatcaaagactgaacaaactctattcttaatttcag

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