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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttcacattttaagtgtcatacagacttttagaattgttgtttctgctattatggcttgtctgagcttatgttctattcattgatttggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGCCCGTGGTGTGCGGAGAG

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 12
-------ctgtttcacattttaagtgtcatacagacttttagaattgttgtttctgctattatggcttgtctgagcttatgttctattcattgatttggataca--tagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGCCCGTGGTGTGCGGAGAG--------------------------------
        | ||| ||||||||| || ||||   | ||| | || || |  || ||| || ||             | || || |  |  ||||||||| |     |||||||||||||| ||| ||| ||||||||||||| |||||||| ||| | ||||||||||| |||||||                                
gctgcgcttttttgacattttaattgccatattaagtttcataactgct-cttatgcaataataat--------agtaatcttgttcttgttgatttgggtgtgattagGCGTCAGATTGCAAATCCAGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGGTCATTTCTTATCGTCAACATTGACTTAATTA

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 12
-------ctgtttcacattttaagtgtcatacagacttttagaattgttgtttctgctattatggcttgtctgagcttatgttctattcattgatttggataca--tagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGCCCGTGGTGTGCGGAGAG
        | ||| ||||||||| || ||||   | ||| | || || |  || ||| || ||             | || || |  |  ||||||||| |     |||||||||||||| ||| ||| ||||||||||||| |||||||| ||| | ||||||||||| |||||||
gctgcgcttttttgacattttaattgccatattaagtttcataactgct-cttatgcaataataat--------agtaatcttgttcttgttgatttgggtgtgattagGCGTCAGATTGCAAATCCAGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG
















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|58655643|gb|CK044323.1|CK044323
EST:     CTGGGAGCGAGGGA-GCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CTGGGAGC-ACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|86483283|gb|CI125916.1|CI125916
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58675521|gb|CK064208.1|CK064208
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|66913089|gb|CX099937.1|CX099937
EST:     CTGGGAGCACAGAAGCGACCACTTTGGAGGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CTGGGAGCACAGAAGCGACCACTTTGGA-GGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|29630757|gb|CB635766.1|CB635766
EST:     GGAGCACAGAAGCGACCCCTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTTTGGC
genomic: GGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|29627088|gb|CB632099.1|CB632099
EST:     TTTGGGGGCAAGCAGAACCCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCCCACGCACACTAACCTCTCTGGC
genomic: TTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|218501369|gb|FG965487.1|FG965487
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|88411135|gb|CI606354.1|CI606354
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAG
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAG
EST: gi|29683055|gb|CB679330.1|CB679330
EST:     TTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: TTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACA
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACA
EST: gi|29622204|gb|CB627215.1|CB627215
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|29644040|gb|CB649047.1|CB649047
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgctattatggcttgtctgagcttatgttctattcattgatttggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGCCCGTGGTGTGCGGAGAG
                                    cattgat  putative branch site (score: 4)
                                tattcatt  TA-rich tract