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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_Os02g42320.1
intron # 3
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|27554138|gb|CA998038.1|CA998038
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|27576119|gb|CA998813.1|CA998813
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|86493119|gb|CI135752.1|CI135752
EST:     CTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: CTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|396941624|gb|HO188281.1|HO188281
EST:     AAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: AAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|25797837|gb|CA753798.1|CA753798
EST:     AAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: AAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
EST: gi|56550165|gb|CX056269.1|CX056269
EST:     GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG                         TGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC
genomic: GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAGgtaacctttt ... cttctttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGC


 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