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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagagctagactcgactatgtctagaagtatatgctagctacataatacgaactgatgagttattaatatatatttgactggtcgatactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTCACTTGAAAGGCAGCTAGATTCGTCTTTGAAACAAATCAGATCAATAAGG

Basic information

species Glycine max
transcript GLYMA11G36890.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaagagctagactcgactatgtctagaagtatatgctagctacataatacgaactgatgagttattaatatatatttgactggtc-gatactcat-tagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTCACTTGAAAGGCAGCTAGATTCGTCTTTGAAACAAATCAGATCAATAAGG
              |  ||||    |||     |  |||| || || |    |   || |   ||| ||  || | |||||  | |  |||  | |  |||||| ||  |||||||||||||||| |||||||| |  || ||||||||||||||||| || ||||| ||||| || ||||| || |||||| |  | |||
-------------gtaaactaa--ttagcttcttcagctaccttcagagagtgt-ttgtttttttagtag-atttttttgatggttttgatgttgaaatagGAATCTGTTGGGAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGAGTCACTTGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCAGAGCTCTCAGG
















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|208095699|gb|GD897161.1|GD897161
EST:     AATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGC
genomic: AATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGC-GTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGC
EST: gi|208215171|gb|GE011038.1|GE011038
EST:     GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|208324622|gb|GE125755.1|GE125755
EST:     GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAG
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAG
EST: gi|208029699|gb|GD832077.1|GD832077
EST:     AATACTCGAGGCTAGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAACAAAGAGCTTGAGTC
genomic: AATACTTGAGGCT-GAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|208032034|gb|GD827720.1|GD827720
EST:     GAATACTCGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAACAAAGAGCTTGAGTC
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|193323165|gb|FK291571.1|FK291571
EST:     GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|18734332|gb|BM528121.1|BM528121
EST:     GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|193414144|gb|FK376178.1|FK376178
EST:     GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|193490532|gb|FK457701.1|FK457701
EST:     AGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
genomic: AGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|208245120|gb|GE039008.1|GE039008
EST:     AATACTCGAGGCTAGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAACAAAGAGCTTGAGTC
genomic: AATACTTGAGGCT-GAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|193338866|gb|FK302589.1|FK302589
EST:     GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
genomic: GAATACTTGAGGCTGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC
EST: gi|208252055|gb|GE049288.1|GE049288
EST:     GAGGCTAGAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAG                         GAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAACAAAGAGCTTGAGTC
genomic: GAGGCT-GAAAGCGCGTTATGAAGCTCTTCAGCGTTCTCAAAGgtaaagagct ... tactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatacgaactgatgagttattaatatatatttgactggtcgatactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTCACTTGAAAGGCAGCTAGATTCGTCTTTGAAACAAATCAGATCAATAAGG
            tgatgagttattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagagctagactcgactatgtctagaagtatatgctagctacataatacgaactgatgagttattaatatatatttgactggtcgatactcattagGAACCTTATGGGAGAAGATCTTGGTCCTCTAAGCAGCAAAGAGCTTGAGTCACTTGAAAGGCAGCTAGATTCGTCTTTGAAACAAATCAGATCAATAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA