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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttcctatgttaccagaacctgttgtttgattatatgatatatggcctgtttattgcattctaatctctttaaaaaatgttttttttcccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAGCCCTAAAGCTCTTATTTGGGGTAAAACTCCCAAACTTGTCGGGGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g25189.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25189.6 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G473533_T06 (Zea mays), 3'ss of exon 10
gtactcttcctatgttaccagaacctgttg--tttgattatatgatatatggcctgtttattgcattctaatctc----tttaaaaaatgttttttttcccatcca-----cagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAGCCCTAAAGCTCTTATTTGGGGTAAAACTCCCAAACTTGTCGGGGGAAAG
||||||||  | | |  ||||||  |      | |    || ||||||||  ||||||| ||||||| |||  |     | || |   | |    | |  |||        |||||| || |||||| ||||||| || || ||||||||||| |||||||||  ||| ||||||| ||| ||||| ||| |||||||| ||||||||||||||
gtactcttggtttttctccagaatatcaaagctatagcaatttgatatata-cctgtttcttgcattgtaactttgttgtctacatgctataccatgtggcatgtggtactcagCTACCTAGTGTTCCGAGGAGCTAACAAGCAAAAACATGTGTTCAAGAAGGACCCCAAAGCTCCTATATGGGGAAAACCTCCCAAAGTTGTCGGGGGAAAG

upper sequence: LOC_Os01g25189.6 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G473533_T05 (Zea mays), 3'ss of exon 9
gtactcttcctatgttaccagaacctgttgtttgattatatgatatatggcctgtttattgcattctaatctc----tttaaaaaatgttttttttcccatcca-----cagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAGCCCTAAAGCTCTTATTTGGGGTAAAACTCCCAAACTTGTCGGGGGAAAG
      |  | |   || || | |      | |    || ||||||||  ||||||| ||||||| |||  |     | || |   | |    | |  |||        |||||| || |||||| ||||||| || || ||||||||||| |||||||||  ||| ||||||| ||| ||||| ||| |||||||| ||||||||||||||
-----ttctccagaatatcaaagc------tatagcaatttgatatata-cctgtttcttgcattgtaactttgttgtctacatgctataccatgtggcatgtggtactcagCTACCTAGTGTTCCGAGGAGCTAACAAGCAAAAACATGTGTTCAAGAAGGACCCCAAAGCTCCTATATGGGGAAAACCTCCCAAAGTTGTCGGGGGAAAG
















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|33689268|gb|CF317507.1|CF317507
EST:     TGCTACAGTTAACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: TGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|58679610|gb|CK068297.1|CK068297
EST:     GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|88840388|gb|CI079842.1|CI079842
EST:     GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATNGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|87015902|gb|CI279654.1|CI279654
EST:     GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|88227443|gb|CI226923.1|CI226923
EST:     AACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAATACATGTCTTCAAGAAGAG
genomic: AACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcctgtttattgcattctaatctctttaaaaaatgttttttttcccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAGCCCTAAAGCTCTTATTTGGGGTAAAACTCCCAAACTTGTCGGGGGAAAG
               ttctaat  putative branch site (score: 2)
                                  tgttttttttcccatc  putative PPT
              attctaatctctttaa  TA-rich tract