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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcagacatttcagtgtgttatatatctgcctcctaactgatgactataaggattgagaagtatcagtctaatatttgtcaatattgtcctctttccagTTCATTTTGCTTGGAGCTGTTCCATTCCGTAGGGATGTTCCTCGGTTGCAGAAGCTTGGGGTGTATGGTGTCATAACCCTGAATGAACCATTTGAGACTT

Basic information

species Oryza sativa
transcript LOC_Os06g05870.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05870.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G863550_T01 (Zea mays), 3'ss of exon 1
--------tagcagacatttcagtgtgttatatatctgcctcctaactgatgactataaggattgagaagtatcagtctaatatttgtcaatattgtcctcttt-ccagTTCATTTTGCTTGGAGCTGTTCCATTCCGTAGGGATGTTCCTCGGTTGCAGAAGCTTGGGGTGTATGGTGTCATAACCCTGAATGAACCATTTGAGACTT
         |||||  ||     | | |   || ||||  |    |||  |  ||||     ||||||      | |     |  ||  | ||||| | | | | ||||||| ||||||| ||||| ||||||||||| || |||||  | || || |||||||||||| | | |||||| |||||| | |||||||||||||||||||
ttgtgcttgagcagctatca-gatatttggcatttctgtttaactactcgtagctatct---ttgaga-----taatgatgcagatgcaattattgacttttgtgccagTTCGTTTTGCTCGGAGCGGTTCCATTCCGCAGCGATGTAACACGCTTACAGAAGCTTGGGATATGTGGTGTGATAACCTTAAATGAACCATTTGAGACTT
















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|58693134|gb|CK081821.1|CK081821
EST:     AGGTCCAGGCCGAGTTCCGGTGGTGGGACGAGGTCGATCAG                         TTCATTTTGCTTGGAGCTGTTCCATTCCGTAGGGATGTTCCTCGGTTGCAG
genomic: AGGTCCAGGCCGAGTTCCGGTGGTGGGACGAGGTCGATCAGgtgagctgta ... ctctttccagTTCATTTTGCTTGGAGCTGTTCCATTCCGTAGGGATGTTCCTCGGTTGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataaggattgagaagtatcagtctaatatttgtcaatattgtcctctttccagTTCATTTTGCTTGGAGCTGTTCCATTCCGTAGGGATGTTCCTCGGTTGCAGAAGCTTGGGGTGTATGGTGTCATAACCCTGAATGAACCATTTGAGACTT
                      gtctaat  putative branch site (score: 3)
                                      tattgtcctctttcc  putative PPT
                         taatatttgtcaatat  TA-rich tract