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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaaatagttgtacggactttgcttctattctagtccaacctatctgcaattgtcttctaatagctacttatgatctcagGTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGACCCTCCTTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGAT

Basic information

species Oryza sativa
transcript LOC_Os06g03760.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 8
gtatgtgtaaatagttgtacggactttg-cttctattctagtccaacctatctgcaat-tgtcttctaatagctacttatgatctcagGTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGACCCTCCTTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGAT
           |   || |     |||| | | |||| || || |  | || | |||  ||   |||   |  |  || || |  |||||||||| | || || |||||||||||||||||||||||||||||||||||||| |||||| | || || |||||||||||| ||||| |||| ||||||
----------gtgagtgcaaaacttttgtcctgtattttaatcaagtcaatttccaaagtgatctcttcaaaatg-ttgtgcttgcagGTTAATTGTTTCAATAGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGAT

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 6
gtatgtgtaaa-tagttgtacgg-actttgcttctattctagtccaacctatctgc--aattg-tcttctaatagc-tacttatgatctcagGTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGACCCTCCTTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGAT
||  ||| |||    |||| | | ||||  ||| | |  || || |   ||  | |  ||||| |||  | | | | |  || || |  |||||||||| | || || ||||||||||||||||| |||||||||||||||||||| |||||| | || || |||||||||||| ||||| |||| ||||||
gtgggtgcaaaacctttgtgctgtacttgtcttgtttcttaatcaagtgtactttcccaattgatctgttcaaaacattgttgtgcttgcagGTTAATTGTTTCAATAGCTTGGGTTGCACATATTGTCATATACTTGTTGATTGATCCTCCTCTATCTTCTTTCCTGAATGAAGTCTTCATAAAGTTGGAT

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtgtaaatagtt--gtacggactttgcttctattctagtcca-acctat-ctgcaattgtcttctaatagctac------ttatgatc-----tcagGTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGACCCTCCTTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGAT
|      ||  |||||  ||  ||  ||| |||||  | || |      |||| ||   |  | | | ||  || | |       | || |      | ||||| ||| | ||  | |||||| |||| |||||||||||||| ||| ||||||| |||||| ||||  | ||| | |||||  | ||| | ||  | |||
gctcacctac-tagtttggtgtggtttttacttcttatttactatgtgtctattctctgaaggacctttacaagttgcatttctctttgtttgtttattagGTTGATTGTTTCAGTGGCTTGGATTGCTCATATCGTCATATATTTGCTGATTGATCCTCCTCTGTCTCCTTTCTTAAATGAGGTTTTCATCAAGCTAGAT

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|58684950|gb|CK073637.1|CK073637
EST:     GCTTTGACAGTTCTTGGTTACATTGGAAAACTTTTATTTGGTGCTGTCGG                         GTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGAT
genomic: GCTTTGACAGTTCTTGGTTACATTGGAAAACTTTTATTTGGTGCTGTCGGgtatgtgtaa ... atgatctcagGTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattctagtccaacctatctgcaattgtcttctaatagctacttatgatctcagGTTAATTATATCGATTGCTTGGGTTGCACATATCGTCATATACTTGTTGATTGACCCTCCTTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGAT
                              ttctaat  putative branch site (score: 2)
                              ttctaata  TA-rich tract