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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgggatttatactgcctcaagagttgcattaattgttcaatagatttgtccatgttattgactgctctgttgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 11
gtatgcttgggatttatactgcctcaagagttgcattaattgttcaatagat-ttgtccatgttattgactgctctgttgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAG
|||  |||||||||| ||||| | |     |    |||  |||||| | | |  | |||||| | || |     |  ||  | |||  ||||||| ||||||||||| |||||||| ||||||||  |||| ||||| ||||||||||||||||| ||||||||||||||
gtaaacttgggatttgtactgtcac-----tcattttatgtgttcagtggttgctttccatggtgttca-----caattattgtttgtatagGTTTTGGGAGCCTACTTATGAAGACTGCTTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G063851_T01 (Zea mays), 3'ss of exon 11
gtatgcttgggatttatactgcctcaagagttgcattaattgttcaatagat-ttgtccatgttattgactgctctgttgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAG
|||  |||||||||| |||||||||     ||   |||  |||||| | | |  | || ||| |  | |        ||  | |||  ||||||| ||||||||||| |||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||
gtaaacttgggatttgtactgcctccca--ttttcttatgtgttcagtggttgctttctatggtggtca-----aaattattgtttgtatagGTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 9
gtatgcttgggatttatactgcctcaagagttgcattaattgttcaatagat-ttgtccatgttattgactgctctgttgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAG
|||  |||||||||    |  ||       ||   |||| |||||| | | |  | | |||| | || |     |  ||  | |||  ||||| | ||||||||||| |||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||
gtaaacttgggatt----ccaccc-----attttcttaagtgttcagtggttgcttttcatggtgttca-----caattattgtttgtatagGCTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG

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|117245193|gb|CT843395.1|CT843395
EST:     GTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAAGATTGCTTAAATTTGATAGCT
genomic: GTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAA-GATTGCTTAAATTTGATAGCT
EST: gi|38470398|gb|CF954529.1|CF954529
EST:     GTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA                         GTTCTGGGAGCCTACCTATAAAGATAGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgttcaatagatttgtccatgttattgactgctctgttgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAG
                          tattgac  putative branch site (score: 2)
                                           ctatttt  putative PPT
                                        ttgctattttaata  TA-rich tract