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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 7
gtaag-cggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
|||||  | ||  | ||| | |   ||||||    ||| || |      ||| |  || |  |   ||  |        || |||||||    | | ||   |||||||| ||||||| |||||||||||||| ||||||||||| ||||||||||||
gtaaggtgtctcaaatttttattgccattttaaaaaaggttttcaa--gccaacaaggtcctttcagttcacac-----tgtcttacaagaactatttg---gacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G835235_T03 (Zea mays), 3'ss of exon 7
gtaagcggctggattttctttgcacattttggggaagtttgttgttt---accaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
         |    | |||| |    || | || | |||| || |||     || |    |   | || |  |  ||    |  |||||||    | |   ||| ||||||| ||||||| |||||||||||||| |||||||| || ||||||||||||
--------gtatggtgtcttcgatatttattggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactat---ttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
















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|33381492|gb|CF196835.1|CF196835
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58606572|gb|CK034605.1|CK034605
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58590369|gb|CF988677.1|CF988677
EST:     TGGGCATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58673993|gb|CK062679.1|CK062679
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         GCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATC
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATC
EST: gi|218498670|gb|FG952679.1|FG952679
EST:     TGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     TTGAGATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58672614|gb|CK061300.1|CK061300
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|218486932|gb|FG950343.1|FG950343
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGTTGAAAGTGGTGTAGACCAACTTGTGGA
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGA
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58679239|gb|CK067926.1|CK067926
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|29677191|gb|CB673466.1|CB673466
EST:     GCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: GCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|66918477|gb|CX105325.1|CX105325
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
EST: gi|2317500|gb|C22554.1|C22554
EST:     TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAG                         CCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
genomic: TTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggct ... tgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
                            gccttac  putative branch site (score: 3)
                                        ttttctgttc  putative PPT
                                   aattgtttt  TA-rich tract