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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacatgtttacttacctgtgcacttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG

Basic information

species Oryza sativa
transcript LOC_Os02g42320.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------------tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacat-gtttacttacctgt---gcacttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
                                                                                     |||||  |  |||||     ||||      | |             | |  ||        || || ||   |  || |   || | |   ||| |  |||||||||||||||||| ||||| |||||||| |||||||||||||| || || |||||||||||||||||||||||||||
gtactacactgtcttggttgatcttgtattcatttttattttctattttggaatcagaatacattacattacaattgtggtgaagtttaatgtgattgttga--agttatggactttaatgcatcatctcaattgccaagcctttctctatcatgttttattcatgcacttttcttgcattgttttcagTGGGATGGGTCCAGATTTTCGTGTTCTGGTGAGAAAAAGTCGAAAGCAGGCACAGCAGTATTATCGGTTGTACAAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G850355_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------------tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacat-gtttacttacctgt---gcacttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
                                                                                |||||  |  |||||     ||||      | ||            | |  ||        || || ||   |  || |   || | |   ||| |  |||||||||||||||||| ||||| |||||||| |||||||||||||| || || |||||||||||||||||||||||||||
gtactacactgttttggttgatcttgtattcatttttattttctattttggaatcagaatacattacaattgtggtgaagtttaatgtgattgttga--agttatggactttagtgcatcatctcaattgccaagcctttctctatcatgttttattcatgcacttttcttgcattgttttcagTGGGATGGGTCCAGATTTTCGTGTTCTGGTGAGAAAAAGTCGAAAGCAGGCACAGCAGTATTATCGGTTGTACAAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------tttaaattatttgttagtt--tgttacatctctcagcttgctgctgttaatatcagttgcaa----ttcaataatacat---gtttacttacctgt---gcacttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
                                                                          || || ||   |||| |||  ||||  |  | |   | |   |    |  | ||| |||  |    ||   ||  || |    || |   || | |   ||| |  |||||||||||||||||| |||||||||||||| ||||| |||||||| || || ||||| || ||||||||||||||||||
gtactgcactatcttttttgatcttgtattcatttaaattttctattttggaattggaatacattacaattgtgttgaagttcaatgttggttgttgttgaagttatggacctttagtgcatcttctcaattgtcaagttttttctatcacgttctattcatgcacttttcttgcattgttttcagTGGGATGGGTCCAGATTTCCGTGTTCTGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115948_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------tttaaattatttgttagtt--tgttacatctctcagcttgctgctgttaatatcagttgcaa----ttcaataatacat---gtttacttacctgt---gcacttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
                                                                          || || ||   |||| |||  ||||  |  | |   | |        |  | ||| |||  |    ||   ||  || |    || |   || | |   ||| |  |||||||||||||||||| |||||||||||||| |||||||||||||| || || ||||| || |||||| |||||||||||
gtactgcactatctttgttgatcttgtattcatttaaattttctattttggaattggaatacattacaattctgttgaagttcaatgttggttgttgttgaagttatggacctttaatgcatcttctcaattgtcaagttttttctatcacgttctattcatgcacttttcttgcattgttttcagTGGGATGGGTCCAGATTTCCGTGTTCTGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATTGGTTGTACAAG

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacatgtttacttacctgtgcacttc----tttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
|||   |||    || | |   || |  |   |  |   |    ||||  |   |||||| |   | ||  |  |  || ||  | |   |||     ||||||||| |||||||||||||| || ||| | ||  |||||||  ||||||||||  |||||||| ||||||| || || 
tttctgttaagcttttggtaaatagaaat---aattatgtatccttaacttgtcttgcaaatatcttatttac-tagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 5
---tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacatgtttacttacctgtgcacttct-ttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
    |||   ||  | ||   ||  |   | |   || ||   ||   |   |  | ||     ||  |||    |  || |  |  ||  |  |  | |||||||| |||||||||||||| || ||| | ||  |||||||  ||||||||||  |||||||| ||||||| || || 
aggcttagtctacctttt---ttaatttctgttaaagtttttggcaaatggaaataattatttgtccttaacttgt-cttgcaaatttggtctttgttgttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCCGAGCAGTATCATCGGTTATATAAA

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 5
-tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacatgtttacttacctgtgcacttc----tttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
 ||    ||| || || ||   |   |      || |  ||    ||||  |   |||||| |   | ||  |  || || ||  | |   |||     ||||||||| |||||||||||||| || ||| | ||  |||||||  ||||||||||  |||||||| ||||||| || || 
tttctgtttagtttttggtaaatagaaat----agttatctatccttaacttgtcttgcaaatatcttatttac-ttgacctaaatatagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

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|88344734|gb|CI624385.1|CI624385
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAG
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAG
EST: gi|58594931|gb|CF993239.1|CF993239
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88394630|gb|CI605971.1|CI605971
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAAAATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|87011125|gb|CI287802.1|CI287802
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|58599900|gb|CK010428.1|CK010428
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|428178|gb|D24326.1|D24326
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGNGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGA
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGA
EST: gi|86848618|gb|CI293933.1|CI293933
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTC
EST: gi|88299773|gb|CI577275.1|CI577275
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCG
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCG
EST: gi|88305149|gb|CI652087.1|CI652087
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAA
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAA
EST: gi|58590935|gb|CF989243.1|CF989243
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88309484|gb|CI655852.1|CI655852
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88412151|gb|CI573427.1|CI573427
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGA
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGA
EST: gi|33680962|gb|CF309201.1|CF309201
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAAC-TTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88444698|gb|CI694934.1|CI694934
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGT
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGT
EST: gi|88397120|gb|CI593332.1|CI593332
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|55413225|gb|CV725601.1|CV725601
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88421484|gb|CI618608.1|CI618608
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|86848709|gb|CI293996.1|CI293996
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88577098|gb|CI673653.1|CI673653
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTT
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTT
EST: gi|88578215|gb|CI687134.1|CI687134
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCC
EST: gi|88395675|gb|CI590690.1|CI590690
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCC-GATTTCCGTGTT
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTT
EST: gi|88414830|gb|CI604188.1|CI604188
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|55413193|gb|CV725569.1|CV725569
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88355030|gb|CI615911.1|CI615911
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88426118|gb|CI604407.1|CI604407
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGA
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGA
EST: gi|88320096|gb|CI639459.1|CI639459
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|88340299|gb|CI652648.1|CI652648
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGT
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGT
EST: gi|88353714|gb|CI633105.1|CI633105
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatcagttgcaattcaataatacatgtttacttacctgtgcacttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG
                               tacttac  putative branch site (score: 1)
                                           cacttctttc  putative PPT
             aattcaataatacat  TA-rich tract