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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttgactttattctctgatattttgactatgtattggttcatacactgtaactaagattatttatgttcttatgcttctgtttttctgtcttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAAT

Basic information

species Oryza sativa
transcript LOC_Os11g25980.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 2
tattttgactttattctctgatattttgactatgtattggttcatacactgtaac-taagattatttatgttcttatgcttctgtttttctgtcttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAAT
| || ||   |   ||| | ||| ||||||||     |||   |   | |       ||| |||| ||   | |    |   ||| ||| |  |||  |||| ||||| ||  |||||||| |||||||||| |||||||| ||||| ||||| || || || || || || ||||| |||||||||||||||||||||||
tgttctggtctaggtctataatagtttgactaaactctggagtagttaataccgtgcaagtttatataacctttctgacacttgtattttta-ctttacagAATTCAGGTTCCTGAAAAGGTTGATTCTTGTTCATGGGCGGTACTCCTACAATCGCACTGCCTTCCTGTCGCAGTACTCTTTCTACAAGTCATTGTTAAT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 20
tattttgactttattctctgatattttgactatgtattggttcatacactgtaactaagattatttatgt-tcttatgcttctgtttttctgtc--ttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAAT
 | ||  |          || | |||     ||   ||  ||  |    | | |||   |   || || | ||| ||| |    || ||||||   ||  ||||||| |||||  |||| ||  | ||||| |||||||| || ||||| |||||||||||||| ||||||||||| ||||| ||||| |||||  |  | ||
-aattatataaggcagattggtgtttc--tcattgtttcattagttgcttatgactgcaagatttcatctctctgatgttatgattgttctgttaattttcagAGTTTAGATTCCTGAAGAGATTAATTCTGGTCCATGGCCGCTACTCCTACAACCGTACAGCATTTCTTTCTCAATATTCATTCTATAAGTCCCTACTGAT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 20
tattttgactttattctctgatattttgactatgtattggttcatacactgtaactaagattatttatgttctt-atgcttctgtttttctgtc--ttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAAT
 | ||  ||         || | | |     ||   ||  ||  |    | | |||   |   || |||||  | ||| |   ||| ||||||   ||  ||||||| |||||  |||| ||  | ||||| |||||||| || ||||| |||||||||||||| ||||||||||| ||||| ||||| |||||  |  | ||
-aattatacaaggcagattggtgtctc--tcattgtttcattagttgcttatgactgcaaaatttcatgtttctgatgttatggttgttctgttaattttcagAGTTTAGATTCCTGAAGAGATTAATTCTGGTCCATGGCCGCTACTCTTACAACCGTACAGCATTTCTTTCTCAATATTCATTCTATAAGTCCCTACTGAT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 20
lower sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 19
tattttgactttattctctgatattttgactatgtattggttcatacactgtaactaagattatttatgttcttatgcttctgtttttctgtcttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAAT
  |   || | |||   |  ||| | ||  ||| |    | | ||||   | ||  ||  |    |  ||||||      ||  | ||   |    ||||  ||||| ||| | ||||| ||||||||||| |||||| | || ||||| ||||| ||||| ||| | || |||||||| |||||||| || ||||| ||
-gtaaggaatatatgtac--ataatatg--tatcttcaagctaataccaaggaaacaatttctgattggttcttgctggactactctttgatt---gcagGATTCAGGTTTCTAAAAAGACTGATTCTTGTTCATGGGAGGTATTCATATAACCGGACAGCATTTTTGTCCCAGTATTCCTTCTACAAATCGTTGTTGAT

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|163929268|gb|EG711029.1|EG711029
EST:     TGGCAGAGAAGGTCTTCAAGCAGCAAGGGCTGCTGACTATAGCGTTGGCA                         AGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACA
genomic: TGGCAGAGAAGGTCTTCAAGCAGCAAGGGCTGCTGACTATAGCGTTGGCAgtaagtcttt ... gtcttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgtaactaagattatttatgttcttatgcttctgtttttctgtcttggcagAGTTCAGATTTTTGAAAAGGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAAT
   ctgtaac  putative branch site (score: 3)
                                cttctgtttttctgtc  putative PPT
          taagattatttatgtt  TA-rich tract