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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgatttttgtgctcacactgagcttttgctgtatatttttatgtaagaaataatttaattaatttctttggcactaacaatactataatttatgcagGCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCCGATCTGAGTGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGG

Basic information

species Oryza sativa
transcript LOC_Os01g40620.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40620.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0066g02600.t01 (Vitis vinifera), 3'ss of exon 8
---ttttgatttttgtgctcacactgagcttttgctgtatatttttatgtaagaaataatttaattaatttctttggcactaacaatactataatttatgcagGCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCCGATCTGAGTGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGG
   |    | | || || | |  |||    |    |||| | |    | |    |||  | |  ||   || | |     |||  |   || |||| ||||||||||| || || || ||||||||  ||||||||||||| ||||| || || ||||| ||||| ||||||||||||||||| ||||| || || ||| | |
ttatgcccaatcttctgatgatcctgcctctaacttgtaaactaactttt---caattctctgtttggcttttgttttcttaatcaatataaaattcatgcagGCAATTCGGAAACATAAGTTTGTCAACATATTGGATAATCCTGGGTCTGCTGATCTCAGTGCATATGTTGATTTTGCATCCATCAGGCATTCTGCTGAAG
















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|29661500|gb|CB657775.1|CB657775
EST:     CACTTATCATTGACTACGGAAAAGATGGAATAGTCTCTGATAGTCTTCAG                         GCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCC
genomic: CACTTATCATTGACTACGGAAAAGATGGAATAGTCTCTGATAGTCTTCAGgtttggatat ... atttatgcagGCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCC
EST: gi|29644655|gb|CB649662.1|CB649662
EST:     CACTTATCATTGACTACGGAAAAGATGGAATAGTCTCTGATAGTCTTCAG                         GCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCC
genomic: CACTTATCATTGACTACGGAAAAGATGGAATAGTCTCTGATAGTCTTCAGgtttggatat ... atttatgcagGCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCC
EST: gi|29644656|gb|CB649663.1|CB649663
EST:     CACTTATCATTGACTACGGAAAAGATGGAATAGTCTCTGATAGTCTTCAG                         GCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCC
genomic: CACTTATCATTGACTACGGAAAAGATGGAATAGTCTCTGATAGTCTTCAGgtttggatat ... atttatgcagGCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagaaataatttaattaatttctttggcactaacaatactataatttatgcagGCAATCCGCAAGCACAAGTTTGTACACATATTGGATAACCCTGGTTCAGCCGATCTGAGTGCTTATGTTGATTTTGCATCAATCAGACACTCCGCTAAGG
                             cactaac  putative branch site (score: 1)
     aaataatttaattaat  TA-rich tract