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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaagccatttttgttatacccatggcttaatgttgagctcaaattagaaaggatttttttattattattaattattgtttgtttcaatacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA

Basic information

species Glycine max
transcript GLYMA09G30910.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g32364.1 (Oryza sativa), 3'ss of exon 1
-aaaaaagccatttttgt-tatacccatggcttaatgttgagctcaaattagaaaggatttttttattattattaattattgtttgttt-caatacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA
 || | ||| |     |  | ||  | |   |   |||  |   | |  | |  ||  |  |  | | |  | | | ||  ||||| ||    | |  | ||||     | ||||||||||  |||| ||| ||| |||||||| |||||||||||||||| 
caacagagcaaagagcgcctctaatcctatatacgtgtaca-tgcgaccttgtgag--tcgtggtgtaaagactgactagagtttgcttatttttctgaccagGTGAAATAGCAAATAATGCTACGGCAGATGTTACTGTTGATGAGTACCATCGCTACAAG
















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|213604894|gb|DB960575.1|DB960575
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|209710515|gb|BW662051.1|BW662051
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGAACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|193650337|gb|FK598092.1|FK598092
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGGAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|208079829|gb|GD874099.1|GD874099
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|213619687|gb|DB965633.1|DB965633
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAA-CCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCT-TTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|208291083|gb|GE081551.1|GE081551
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|193363574|gb|FK331298.1|FK331298
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|193709892|gb|FK642142.1|FK642142
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|208110084|gb|GD907214.1|GD907214
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|192332517|gb|FK025622.1|FK025622
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|298166439|gb|HO009878.1|HO009878
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|209702642|gb|BW652737.1|BW652737
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|209718599|gb|BW674725.1|BW674725
EST:     CAAAGACGGTCGCGGCCCAAGCATTTGGAACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: CAAAGACGGTCGCGGCCCAAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
EST: gi|208092374|gb|GD885491.1|GD885491
EST:     AAGCATTTGGGACGTCTTCATCAAAAAACCCG                         GGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC
genomic: AAGCATTTGGGACGTCTTCATCAAAAAACCCGgttcgtcaac ... tacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagaaaggatttttttattattattaattattgtttgtttcaatacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA
                       tattaat  putative branch site (score: 2)
          atttttttattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaagccatttttgttatacccatggcttaatgttgagctcaaattagaaaggatttttttattattattaattattgtttgtttcaatacaaaacagGGATTGTCGCAAATAATGGCACGGGAGAAGTTTCTGTTGATCAGTACCATCGCTACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
aaaaaag
- - - - - - - - - - - -catggct
- - - - - - - - - - - - - - - - -tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt