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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacattcatttcataaatattttctgttacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G129482_T01 (Zea mays), 3'ss of exon 5
----------gtaag--tatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacat--tcatttcataaatattttctgt-tacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC
          || |   | || |||  |||   ||| |||| || | ||||   | || | |  ||||| ||   ||    ||  ||| |  |  |||  |||   |||| ||  |   |||| ||||||||| || ||||| |||||||||||||| ||||||||||| |||||| |||| ||||| |||||||||||  |||| || || ||||||||||||||||
gtaagtgcatgtcatgttgtacattacatgacagaaatacacatca-ttagccctgtg-cgcc-agttcttgcattagccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G835235_T02 (Zea mays), 3'ss of exon 9
----------gtaag--tatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacat--tcatttcataaatattttctgt-tacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC
          || |   | || |||  |||   ||| |||| || | ||||   | || | |  ||||| ||   ||    ||  ||| |  |  |||  |||   |||| ||  |   |||| ||||||||| || ||||| |||||||||||||| ||||||||||| |||||| |||| ||||| |||||||||||  |||| || || ||||||||||||||||
gtaagtgaatgtcatgttgtacattacatgacagaaatacacatca-ttagccctgtg-cgcc-agttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 10
gtaagtatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacattcatttcataaatattttctgttacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC
                      |||| ||    | |    |||||   || |  |    || |||    ||  ||| ||  |||  |||    ||  ||     |||| |||| |||| ||||||||||||||||||||||||||||||||||| |||||| |||||||||| ||||| ||||||||||| || || ||||| ||||||||||
--------------------gtaagtgcatgccattgtacattat---acatgatg---gaaatacccctgttgactttggttttctaagatcttcatgaatgttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC

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|33381492|gb|CF196835.1|CF196835
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTNNGATGAGCTTCGNGNCNCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|88840799|gb|CI080253.1|CI080253
EST:     GATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: GATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58686738|gb|CK075425.1|CK075425
EST:     AGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: AGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     ATCTTGTCTCTAGGCTGGTCCAGTACTCAACCAAACTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGAACCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|88830876|gb|CI079310.1|CI079310
EST:     GATGCACTGCT                         GTGGAAGCACTTGTTCACCCGTTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: GATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58590369|gb|CF988677.1|CF988677
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAANCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|218498670|gb|FG952679.1|FG952679
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58601780|gb|CK012308.1|CK012308
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTGGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|29618977|gb|CB623989.1|CB623989
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58689596|gb|CK078283.1|CK078283
EST:     CTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: CTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58672614|gb|CK061300.1|CK061300
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|218501699|gb|FG952639.1|FG952639
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|86593838|gb|CI260067.1|CI260067
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|55411037|gb|CV723413.1|CV723413
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|29677191|gb|CB673466.1|CB673466
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|88960574|gb|CI006535.1|CI006535
EST:     GATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: GATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|218501528|gb|FG953636.1|FG953636
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGA
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGA
EST: gi|87038213|gb|CI192835.1|CI192835
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|66918477|gb|CX105325.1|CX105325
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|87007029|gb|CI275337.1|CI275337
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|33691829|gb|CF320068.1|CF320068
EST:     AAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: AAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
EST: gi|2317500|gb|C22554.1|C22554
EST:     ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT                         GTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT
genomic: ATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagtatat ... ctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagataattgtgcagacattcatttcataaatattttctgttacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC
                                  ttttctgttaccttt  CT-rich tract
                acattcatttcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacattcatttcataaatattttctgttacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC