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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g58730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 3
gcaataaaatcttgccgcccactttctttgctctctctccatgaagtac-------cttagcttag----tcaacctgt-tatcttgcac-tgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG
|||||||  | |  | ||||||||||||  | |   | |  |  | | |        |||  ||||    |  || ||  | |||||||  | ||   |  || |   | ||  |||||| | |||||||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||
gcaataatctttccctgcccactttcttgccccggccccggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 5
----gcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG
    |   |    ||||  |    |  |||||| || | |    ||  |||   |    | ||| |  ||| ||   | || |     || |   |||   || | ||||| | |||||| | || ||||||||||||||||| || || || |||||||||||||||||||
gtttgatctgtggtcttctcctgaaacttctttcctgttt---tattcagt--ttacattcagtgattctgatagaatacatttg-gtatcttgcttttgattcttagTGGGTTCCTGAACTGAGACATTATGCTCCTGGTGTTCCCATCATCCTCGTTGGAACAAAGCTTG
















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|218483315|gb|FG958115.1|FG958115
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAAT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAAT
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTC
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|11233552|gb|AU164964.1|AU164964
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|325493533|gb|JG458057.1|JG458057
EST:     TGGACTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTATCTAAAAAG                         TGGATACCTGAA
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAA
EST: gi|88832933|gb|CI369823.1|CI369823
EST:     CAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: CAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|86900291|gb|CI296334.1|CI296334
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGC
EST: gi|25807453|gb|CA763414.1|CA763414
EST:     TGGCCTNTTCTCTGATCAGCAAAGCAAGCTACGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88410858|gb|CI578664.1|CI578664
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATAC-TGAATTA-GGCAT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCAT
EST: gi|30229558|gb|CB967449.1|CB967449
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCNATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAA
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAA
EST: gi|88337442|gb|CI630739.1|CI630739
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGCAATTAAGGCATCATGCTC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTG-AATTAAGGCATTATGCTC
EST: gi|4714260|gb|AU058227.1|AU058227
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|32947879|gb|BP184451.1|BP184451
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGGCCTTTTCTCTGATCAGCGAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|86415824|gb|CI029835.1|CI029835
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCCATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|7134822|gb|AU082691.1|AU082691
EST:     CAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: CAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|25802725|gb|CA758686.1|CA758686
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58591734|gb|CF990042.1|CF990042
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|3763167|gb|AU029919.1|AU029919
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|7134824|gb|AU082692.1|AU082692
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG
                          cactgac  putative branch site (score: 2)
                                          tttctgtt  putative PPT
                                   atatatatttctgtt  TA-rich tract