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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgtcaaacactccaagccttatctgttcttttaagtattatatgatccctttatttttttccttgtatttaatattactattttctaccaaattcagGTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCTGCAGAATCACAATCGGTACAACATTCTTCAAGCAGGTCACAACTACAGC

Basic information

species Oryza sativa
transcript LOC_Os03g19690.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 6
--acatg-tcaaacactccaagccttatctgttcttttaagtattatatgatccctttatttttttccttgtatttaatattactattttctaccaaattcagGTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCTGCAGAATCACAATCGGTACAACATTCTTCAAGCAGGTCACAACTACAGC
  |   | |  |  |   | |||   | |  | ||||  ||  | | |  |||   || |  || | ||   ||| | || | |||  || |    |   ||| ||||||||||||||||||||| ||||||| ||||||||||| |||||||| ||||| |||||| |||||||||||||||||| ||| || ||||| || 
ccatgcgattcatgatatctagctcaacccatgctttagag-gtcacaaaatcttcttttaattattct--aattcagtaattctaccttttttgcatcccagATTTGAAACTGTTGACATGGCAGTGAGGTTGCTTGTACCTATTATTGTGCTACAGAACCACAATAGGTACAACATTCTTCAAGAAGGCCATAACTATAGT

upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G36720.1 (Glycine max), 3'ss of exon 1
acatgtcaaacactccaagccttatctgttcttttaagtattatatgatccctttatt----tttttccttgtatttaatattactattttctaccaaattcagGTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCTGCAGAATCACAATCGGTACAACATTCTTCAAGCAGGTCACAACTACAGC
   ||||   |   | ||   ||||  |     | || || | | |   |   | | |    | ||  || |  ||||||  || | |||  |      |||||||||||||| |||||  |  |    ||  | |||||||||||||||||  |||| ||||| ||||| ||||||||| |  ||   |||||||| ||||| 
tagtgtctcgcgtgcaaa---ttattagggtactcaaatactttgttgactgatcactgatgtattaactcgagtttaattgtatt-tttattgatttgttcagGTTTGAAACCGTTGATCTTACTTCAAGACTGCTTGTACCTATAATTGTCTTGCAAAATCATAATCGATACAACATTATGGAAAAGGGTCACAATTACAGT
















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|25800195|gb|CA756156.1|CA756156
EST:     GGTGGGTTAATTTCAACTACCATTGAGCATGTTATTGCTCCTGATGTCAG                         GTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCT
genomic: GGTGGGTTAATTTCAACTACCATTGAGCATGTTATTGCTCCTGATGTCAGgtattgcttg ... ccaaattcagGTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCT
EST: gi|427961|gb|D24106.1|D24106
EST:     GGTGGGTTAATTTCAACTACCATTGAGCATGTTATTGCTCCTGATGTCAG                         GTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTNTNCT
genomic: GGTGGGTTAATTTCAACTACCATTGAGCATGTTATTGCTCCTGATGTCAGgtattgcttg ... ccaaattcagGTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatccctttatttttttccttgtatttaatattactattttctaccaaattcagGTTTGAAACTGTTGACATGGCAATGAGGTTACTTGTACCTATAATTGTGCTGCAGAATCACAATCGGTACAACATTCTTCAAGCAGGTCACAACTACAGC
                        atttaat  putative branch site (score: 4)
                                      ttttctacc  putative PPT
       tttatttttttccttg  TA-rich tract