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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtttttaattaatcaaataagaatagagttttccctgtgcaaactgtattgtcattactcagaagtgaaaccgtttgttctgccttcactgattaacagGTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG

Basic information

species Oryza sativa
transcript LOC_Os06g49990.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49990.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 13
gtggtttttaattaatcaaa-taagaatagagttttccctgtgcaaactgtattgtcattactcagaagtgaaaccgtttgttctgccttcactgattaacagGTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG
|||| | ||| |  |||| | |   |||     |  ||||||| | |               ||||| |||| | ||| |    |   || |  | | || |||| |||||||| ||||||||||||||||| |||||||| ||||||||||
gtgggtgttattagatcacactccaaatctgtgtccccctgtgtata---------------tcagatgtgacatcgtgt----tatttttatgggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG

upper sequence: LOC_Os06g49990.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------gtggtt-tttaattaatcaaataagaatagagttttccctgtgcaaactgtattgtcattactcagaagtgaaaccgtttgttctgccttcactgat-taacagGTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG-------------
                                                                                 || ||  || ||  ||    | | ||| |     ||  | | |||  | |   ||  ||| |  |    || |   ||      |   |  |||||    ||||| ||||| |||||||||||||||||||| || ||||| || || |||              
gtgggttattgatgaatactcaatccatgtgttttgctttggaaacttctttatctattcaaagcaaccaccaccatgttctgattgctttatgtatttcgtta-aatggcacaatcaattttcaatttcttcagt--tta-tgggtgaggagattcttaacaaagatcttgctgatactgcagGTAATGAAGAATGGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATG
















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|88445930|gb|CI549653.1|CI549653
EST:     TCCATTTGGGTCAACTTTTGTCTATGGATATCAGAATATTGCTTTTGAG                         GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG
genomic: TCCATTTGGGTCAACTTTTGTCTATGGATATCAGAATATTGCTTTTGAGgtggttttta ... tgattaacagGTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattgtcattactcagaagtgaaaccgtttgttctgccttcactgattaacagGTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG
                                          cactgat  putative branch site (score: 3)
                                      ccttcact  CT-rich tract
                                             tgattaa  TA-rich tract