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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctgttgtaacaattattgatggttttgatgcttcgtgttggccggttaattacatgtttaattacagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTGGCAATACAGGACCATTTGTAGAGGGCCTAATTCAATACTTAAGAATCTTT

Basic information

species Oryza sativa
transcript LOC_Os01g20860.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G158008_T01 (Zea mays), 3'ss of exon 4
gta-tgttctgttgtaacaattat----tgatg---gttttgatgcttcgtgttggccggttaattacatgtttaattacagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTGGCAATACAGGACCATTTGTAGAGGGCCTAATTCAATACTTAAGAATCTTT
|||  || || ||||| |||| |     |||     | |||| |||||   |||||| |  || |||  ||||| ||| ||||| ||||||||||| |||||||| || ||||| || ||||||||||| ||||||||| | || ||||||||||| ||||||||||| ||||| ||||| |
gtagcgtgcttttgtatcaatgacactatgacacatggtttggtgcttaaggttggctgtatagttaattgttttatttcagGGTGGCATTGATGATGGTGGAGCTGCGTCTGTGAGGGCAATTATGCATTGGCAATACCGAACTATTTGTAGAGGACCTAATTCAATTCTTAAAAATCTGT

upper sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
-gtatgttctgttgtaacaat-tatt-------gatggttttgatgcttcgtgttggccggttaatt--acatgtttaatta-cagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTGGCAATACAGGACCATTTGTAGAGGGCCTAATTCAATACTTAAGAATCTTT
  ||  ||| | |  || | | ||||        |  | |||| | || |       |   ||||    || | | |   |  |||||||| ||||| ||| |||| ||||||||||||||||| || ||||| ||||| ||  | ||||| |  ||||| | ||| |||||| | |  |||||||
gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
















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|1631485|gb|C19214.1|C19214
EST:     AAGGTGCTTCCGGGTTATAATTGTCATACCGCTTTTACCTGGGATTTCAG                         GGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTG
genomic: AAGGTGCTTCCGGGTTATAATTGTCATACCGCTTTTACCTGG-ATTTCAGgtatgttctg ... ttaattacagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTG
EST: gi|88402516|gb|CI598743.1|CI598743
EST:     AAAGGTGCTTCCGGGTTATAATTGTCATACCGCTTTTACCTGGATTTCAG                         GGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGATCCAATTATGGAGTT
genomic: AAAGGTGCTTCCGGGTTATAATTGTCATACCGCTTTTACCTGGATTTCAGgtatgttctg ... ttaattacagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGC-AATTATGCACT-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgatggttttgatgcttcgtgttggccggttaattacatgtttaattacagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTGGCAATACAGGACCATTTGTAGAGGGCCTAATTCAATACTTAAGAATCTTT
                                 ttaattacatgtttaa  TA-rich tract