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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgcttgtttctcttagcactgaaggtttatctaaaactatgttttgcattatgttagtttattgatttggcatctactgtatctctttcattctagTTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGCAAAACCACATTGACCTTGTATTGACCGAGGTCGTAATGCCACGTCTGTC

Basic information

species Oryza sativa
transcript LOC_Os03g17570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G095727_T03 (Zea mays), 3'ss of exon 5
tgcatgcttgtttctcttagcactgaaggttt--atctaaaactatgttttgca-------ttatgttagtttattgatttggcatctactgtatctctttc-attctagTTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGCAAAACCACATTGACCTTGTATTGACCGAGGTCGTAATGCCACGTCTGTC
          |   | |||||| || |  |||  |||||  |  || |     |       ||  |||  || | || | || || | |   |||||| ||| ||| ||||||| ||||||||||||||  | |||||||||| || ||||||||||||||| ||| |||| |||||||||||||| |||||  | |||||  |||| ||
----------taattattagcagtggaaatttgtatctatcatcatctaaaaaagggtaattttagttgtttcagtgttctgacagcaatcctatctccttccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGCAGAACAACATCGACCTTGTATTGACTGAGGTTTTCATGCCTTGTCTATC
















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|29665633|gb|CB661908.1|CB661908
EST:     CTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAG                         TTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTG
genomic: CTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAGgtatgcactg ... ttcattctagTTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTG
EST: gi|29642421|gb|CB647428.1|CB647428
EST:     CTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAG                         TTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGC
genomic: CTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAGgtatgcactg ... ttcattctagTTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGC
EST: gi|29642419|gb|CB647426.1|CB647426
EST:     CTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAG                         TTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGC
genomic: CTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAGgtatgcactg ... ttcattctagTTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcattatgttagtttattgatttggcatctactgtatctctttcattctagTTATCCCTGCTGAAAATGGGCTACATGCATGGCAATGTCTTGAAGATCTGCAAAACCACATTGACCTTGTATTGACCGAGGTCGTAATGCCACGTCTGTC
                  tattgat  putative branch site (score: 3)
                                      tatctctttcattct  putative PPT
      attatgttagtttatt  TA-rich tract