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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattacttaatttatgtttcttattatcttgcatgtgaattgatttgtgaaactggtgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG

Basic information

species Oryza sativa
transcript LOC_Os08g34060.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
gtatgcattacttaatttatgtttcttattatcttgcatgtgaattgatttgtgaaactggtgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG
||||||||  ||||  | ||||    ||||| | ||||||||   | ||||||            | |||||  |||  |||             |||| || |||||||||||||||||| || ||||| || |||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||||||||| |||
gtatgcatgtcttagctgatgtacagtattaccatgcatgtgg--taatttgtt----------catgtcaacttttgcatg-------------aaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG

upper sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 19
lower sequence: PP1S91_96V6.1 (Physcomitrella patens), 3'ss of exon 20
-gtatgcattacttaat-ttatgtttcttattatcttgcatgtgaattgatttgtgaaactggtgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG
 ||   || | ||   | |  ||  |||| |  | |   |      || | || |  ||   |||    |||||  |  | | ||   |     | |         |||||||| |||||||| |||||||| ||||| |||||||||||||| ||||| ||||| || || ||||||||| | ||  | || || || || |||
tgttcacaatgctgcttgtcctgcctcttctggtttcatacaccg-ttaagttctataatgcgtgcagtgtcaaggtcctaacgt---tccgtttctt-----ctccagGGTTACTGGATGGTGAAACGTGCTGTTGGTACAAAAGCTTGTCTGCTGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAG

upper sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 19
lower sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
gtatgcattacttaatttatgtttct-tattatcttgcatg-tgaattgatttgtgaaactgg-tgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG
 | |  ||||    |  | || || | | || |||| || |  |||| | |       ||||  |  | | |||   || | |  | |  |  | |        ||| |||||||||||||||| || ||||| ||||| |||||||| || || ||||| ||||| || || || |||||| | ||    ||||| ||||| |||
-tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcag-tttctaacattacattgatt--------tcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG

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|157650644|gb|EX450278.1|EX450278
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|86870886|gb|CI326712.1|CI326712
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GATTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|88958682|gb|CI096197.1|CI096197
EST:     GCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: GCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|88964786|gb|CI084784.1|CI084784
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|29630515|gb|CB635524.1|CB635524
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|29622067|gb|CB627078.1|CB627078
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|29623531|gb|CB628542.1|CB628542
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|86430572|gb|CI082995.1|CI082995
EST:     TCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: TCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
EST: gi|86499063|gb|CI141696.1|CI141696
EST:     CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA
genomic: CCGATGCGTTCCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatta ... atgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaactggtgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG
                      ttttgat  putative branch site (score: 4)
                                aattgaactataaat  TA-rich tract