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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacctatcactctcgctttctctttttaaatcatatgatatctttttatttttatttttcatgttctcacttcatttgcattctattcttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCTGTCTTGGACGGTACTGCCACCTGGCAATTCATGACCTCATGGGCCGAGA

Basic information

species Glycine max
transcript GLYMA16G29960.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G29960.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G23940.1 (Arabidopsis thaliana), 3'ss of exon 1
atcacc--tatcactctcgctttctctttttaaatcatatgatatctttttatttttatttttcatgttctcacttcatttgcattctattcttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCTGTCTTGGACGGTACTGCCACCTGGCAATTCATGACCTCATGGGCCGAGA
| ||     || |           |     ||||  || | | |      ||     |||||      | | | || |    |||| |    ||     ||| | || ||||| |||||||||||||||||||||||||| ||||| || || ||||| ||||| ||  |||| ||||| || |||| ||||||||||||||
accattaacatgaaaaaaaaagcattacactaaa--atttaaaagaaaaataaaaacattttcacaagtattaattaaccaacatttttcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
















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|24135669|gb|BU926179.1|BU926179
EST:     GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAG                         TTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAGgtaatataat ... ttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
EST: gi|298192747|gb|HO033181.1|HO033181
EST:     GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAG                         TTAACGAAGCTC
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAGgtaatataat ... ttgctcgcagTTAACGAAGCTC
EST: gi|26058947|gb|CA801861.1|CA801861
EST:     GTGGCATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAG                         TTAACGAAGCTCCAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAGgtaatataat ... ttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
EST: gi|10235220|gb|BE804167.1|BE804167
EST:     GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAG                         TTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAGgtaatataat ... ttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
EST: gi|18692765|gb|BM521613.1|BM521613
EST:     GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAG                         TTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAGgtaatataat ... ttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
EST: gi|26058667|gb|CA801581.1|CA801581
EST:     GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAG                         TTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCTTTGCTGGCTGTTCAGgtaatataat ... ttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttttatttttcatgttctcacttcatttgcattctattcttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCTGTCTTGGACGGTACTGCCACCTGGCAATTCATGACCTCATGGGCCGAGA
                    ttctcac  putative branch site (score: 2)
                                     ttctattcttgctc  putative PPT
     tttttatttttcatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcacctatcactctcgctttctctttttaaatcatatgatatctttttatttttatttttcatgttctcacttcatttgcattctattcttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCTGTCTTGGACGGTACTGCCACCTGGCAATTCATGACCTCATGGGCCGAGA

- - - - -cactctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct