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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtacccttttcaaccacctctttctaagtaacttgttcactatgttgtttttttttttttttatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAAAGTCTATGGTGGTTCCATTGAAAACGTCAAGGGTTGCACTGACAAAGTT

Basic information

species Glycine max
transcript GLYMA14G36610.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36610.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G10850.1 (Arabidopsis thaliana), 3'ss of exon 2
------gtatggtacccttt----tcaaccacctct---ttctaagtaacttgttcactatgttgttttttttttt--------ttttatgtgac---agGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAAAGTCTATGGTGGTTCCATTGAAAACGTCAAGGGTTGCACTGACAAAGTT
        |||||  |||||    || |  |  | |   ||  | |  || | || | | |     |  || |||          || || |||    ||||||||||| ||||||||||| ||||| |||||| |||| || |  |||||||| ||||| |||||  | || || || ||||||||||||||    |||
accatatgatggttgcctttgtcttcgatgaaatttggatttgaggcgacgtttttattttaacactcattgtttgattggtggcttgatatgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAAAGTATATGGAGGTTCTCTGGATAAGGTGAAGGGTTGCACTGATGCGGTT

upper sequence: GLYMA14G36610.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g00180.t01 (Vitis vinifera), 3'ss of exon 2
gtatggtacccttttcaaccacctctttctaagtaacttgttcactatgttgttttttttttttttt------atgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAAAGTCTATGGTGGTTCCATTGAAAACGTCAAGGGTTGCACTGACAAAGTT
||     |   | |||  |||  | ||| |  |      |||   | | || || ||| ||||  ||      |||||  |||||||| || || |||||||| |||||||||||||||||||| |||||| |||| || ||||| ||  | || |||||||||||||||||  |   | | 
gttcttgaatttcttcctccattttttttttggggggaggttggatttttttttctttgttttaattgctgatatgtggtagGGATCACGCCGGCGGAAACGAAAAGATAAAGCAGCTGGTGCCCGGAATCGAAGTGTACGGTGGGTCTGTCGACAACGTCAAGGGTTGCACCCATCCACTC
















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|209714894|gb|BW682059.1|BW682059
EST:     AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
EST: gi|10847409|gb|BF070096.1|BF070096
EST:     GCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCA
genomic: GCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCAC-TGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCA
EST: gi|4283221|gb|AI440629.1|AI440629
EST:     AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
EST: gi|27426743|gb|CA938263.1|CA938263
EST:     AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
EST: gi|6567238|gb|AW234849.1|AW234849
EST:     AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
EST: gi|298171455|gb|HO016487.1|HO016487
EST:     AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
EST: gi|298196527|gb|HO041270.1|HO041270
EST:     AGCTCGCACGGCCTCACCCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
EST: gi|209706270|gb|BW676285.1|BW676285
EST:     AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTG                         GGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA
genomic: AGCTCGCACGGCCTCACTCTCAAATTCGTCCTCACCACCCACCATCACTGgtatggtacc ... tatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctttctaagtaacttgttcactatgttgtttttttttttttttatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAAAGTCTATGGTGGTTCCATTGAAAACGTCAAGGGTTGCACTGACAAAGTT
         aagtaac  putative branch site (score: 2)
                   ttcactatgttgtttt  putative PPT
                   ttcactatgttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtacccttttcaaccacctctttctaagtaacttgttcactatgttgtttttttttttttttatgtgacagGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAAAGTCTATGGTGGTTCCATTGAAAACGTCAAGGGTTGCACTGACAAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG