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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggtgtttctttcaaaatttcgaataatgttttacaatttttctgtttactttatattttttttgtggtattttttaagtttcaggcatt...

Basic information

species Glycine max
transcript GLYMA02G01750.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggt---gtttctttcaaaatttcgaataatgttttacaat-ttttctgtttactttatattttttttgtggtattttttaagt--ttcaggcatt---------------------------------------------------------------------------------------
|||||| |||||||| |||||||| || || |||||||||||||||   || |||||||||||||||||||| || || |  |||||  |  |    ||    |  ||   ||   || |   | || || | ||| ||||||  |  |  |     |  |  | |||  |    || |  ||    |||                                                                                        
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag

upper sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggtgtttctttcaaaatttcgaa---taatgttttacaatttttctgtttactttatattttttttgtggtatt--ttttaagtttcaggcatt
|||||| |||||||| |||||||| || ||||| ||||| || |||   || ||||||||||||||||| ||  |||| |  ||||| |    | ||    || |||     ||| |||   ||||||        |||| |||    | |    | |||   ||  | |  || |   |     |||| 
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAGgtaaatctcatg----ttttttaggtgtttggaaatttaatgtcaaggccgttttgtgtcatatcttcgctgtttgcatgccagtagttctctatcgtttgcat-

upper sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcag---caccttggtgtttctttcaaaatttcgaataatgttttacaatttttc--tgtttactttatatt-ttttttgtggtattttt-taagtttcaggcatt-----------------------------------------------------------
|||||| ||||||||||||||||| || || |||||||| |||||   |||||||||||| || ||||||||  | || |  |||||      ||||||| |   |||  | |         |  | ||  |  | |||||    ||||| |   |   |||| | ||||||        |||      ||                                                            
GTGTGGCCACTGCAAAAAGCTTGCCCCCGAGTATGAAAAACTTGGCGCCAGCTTCAAGAAGGCTAAATCTGTACTGATAGCAAAGgtacatctcaccttgtttagtctccccaggggaatgttggtattgcaacagttttcatcatttacatcccacaattttctatggtatcgaaacttgttctgaatatctaattacatttctttgctgcaatgaattaactgttttcctttttgtatctactacctag

upper sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggtgtttctttcaaaatttcgaataatgttttacaatttttctgtttactttatattttttttgtggtattttttaagtttcaggcatt
|||||| |||||||| || ||||||||||| ||||||||||| ||    ||||||||||| || || ||||| || || |  ||||| ||     || | | | ||||   |||  |    |   |||| ||  |   ||  |  |  |   || |||     | | | ||  | |  ||     
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtg---tgat-tctatttcggtattcagctccaatgtttaaaagatagatgaatgataga---ttgtttcaacttgtgtattgtggtgaag-----

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|193602208|gb|FK558877.1|FK558877
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193350926|gb|FK314206.1|FK314206
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCCGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|208324590|gb|GE120963.1|GE120963
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193641401|gb|FK589007.1|FK589007
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193494709|gb|FK458903.1|FK458903
EST:     AAGCTTGGTAGCAGCTTCAAGAAAGCCTAAATTCCGTTTTAATCGGCAAG                         GTTGACTGTGAT
genomic: AAGCTTGGTAGCAGCTTCAAGAAAGCC-AAAT-CTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGAT
EST: gi|192333634|gb|FK026879.1|FK026879
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193481517|gb|FK446440.1|FK446440
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|208127487|gb|GD923931.1|GD923931
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193382421|gb|FK349006.1|FK349006
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAAGCACAAGAGTT
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGA-GCACAAGAGTT
EST: gi|193475513|gb|FK440292.1|FK440292
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACA
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACA
EST: gi|208297750|gb|GE092853.1|GE092853
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|208061547|gb|GD859261.1|GD859261
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|208287580|gb|GE081716.1|GE081716
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG                         GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|163921267|gb|EH038909.1|EH038909
EST:     AAAAGCTAGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193627766|gb|FK577948.1|FK577948
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|207758702|gb|GD728748.1|GD728748
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193521591|gb|FK477712.1|FK477712
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|208180185|gb|GD973684.1|GD973684
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|207759728|gb|GD734843.1|GD734843
EST:     AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
EST: gi|193465544|gb|FK432477.1|FK432477
EST:     AAGCTTGGTAGCAGACTTACAAGAAAGCCAAATCTGTTTTAATCGGCAAG                         GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG
genomic: AAGCTTGGTAGCAG-CTT-CAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcacct ... tgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggtgtttctttcaaaatttcgaataatgttttacaatttttctgtttactttatattttttttgtggtattttttaagtttcaggcatt

- - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA