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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgtcgtttgcaaacttctccaatgtattacagtcaatttcttatctgcgttatcaatttttcactgtaaagtttaaccttggcatttcctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC

Basic information

species Oryza sativa
transcript LOC_Os03g02380.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
ccttgtcgtttgcaaacttctccaatgtattacagtcaatttcttatctgcgttatcaatttttcactgtaaagtttaaccttggcatttc---ctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC
  || |  ||  |||  || |    | | ||    |  || ||     | |||| || |||| | | | | |  | |    ||    |||    | ||  ||||| || ||||||  ||||||||||||  | |||||||| ||||||||||||||||| ||||| || || || ||| | || ||||| |||| |||  | |
--ttcttatt-acaatgttttttttttttttggtcttgatatccgggttacgttgtctatttatgattctgagttgtctgtttttttttttaaacattgtcagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC

upper sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 3
------ccttgtcgtttgcaaacttctccaatgtattacagtcaatttcttatctgcgttatcaatttttcactgtaaagtttaaccttggcatttcctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC
       ||| | |||  |||  || |     || ||    ||   ||||| | | |||| |  |||| | | | | || ||     ||    |   | |   ||||| || ||||||  ||||||||| ||  | |||||||| ||||||||||||||||| ||||| || || || ||| | || ||||| |||| |||  | |
gtgtatacttcttgtt-acaatttttttttg-gtcttgttttc--cttcttgt-tacgttgtgtatttatgattctgaa-ttgcctgtttttttaaacatcgtcagAGGGGCTTTGATCAACAATGGCTATCATTAACATTCTCAAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC

upper sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
--------ccttgtcgtttgcaaacttctccaatgtattacagtcaatttcttatctgcgttatcaatttttcactgtaaagtttaaccttggcatttcctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC
        ||||   ||  |  ||||||   | |   |   |   ||| |  | | ||  || | |  || |    ||    | | |   ||    || |||   ||||| ||||||||   ||| ||||||||  | |||||||| ||||| ||||||||||||||||| ||  | || ||| | || ||  | |||| |||  | |
aaaaaaagccttcgtgtg-gttaacttca--agtagttgggatataatgttgtgt-tgttttgttatattat----gttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC

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|58665406|gb|CK054092.1|CK054092
EST:     CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAG                         AGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
genomic: CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAGgtactggacg ... cctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
EST: gi|40490542|gb|BX899979.1|BX899979
EST:     CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAG                         AGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
genomic: CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAGgtactggacg ... cctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
EST: gi|29656297|gb|CB652572.1|CB652572
EST:     CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAG                         AGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
genomic: CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAGgtactggacg ... cctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
EST: gi|29614295|gb|CB619308.1|CB619308
EST:     CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAG                         AGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
genomic: CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAGgtactggacg ... cctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
EST: gi|58672276|gb|CK060962.1|CK060962
EST:     CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAG                         AGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT
genomic: CGCTGCTCTTCTCGGCGTTCGAGTCATGGCTCGTCGCGGAGCACAACAAGgtactggacg ... cctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgcgttatcaatttttcactgtaaagtttaaccttggcatttcctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC
                            gtttaac  putative branch site (score: 3)
                                        catttcctttc  putative PPT
       ttatcaatttttca  TA-rich tract