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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattacccataatctccttgtcaacatttcctgttcattattgagcaatcagctgcttgctaacgaaataaagtttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAGAGAAAGTGCTCCTTACAGTTAAGCCACAAT

Basic information

species Oryza sativa
transcript LOC_Os08g41390.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 4
gtgattaccc-ataatct-ccttgtcaacatttcctgttcattattgagca-atcagctgcttgctaacgaaataaagtttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAGAGAAAGTGCTCCTTACAGTTAAGCCACAAT------------------
|| |    |  ||  |||  |||  ||   | | |||   ||| ||| ||  ||| | || || |||||       | | |  | ||||| | ||| || ||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||||||| ||||||||||                  
gtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaac------tactgtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAGAGAAGGTGCTCCTTACAGTAAAGCCACAATGTGAGATTCCATTTCAAA

upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G096585_T01 (Zea mays), 3'ss of exon 4
gtgattaccc-ataatct-ccttgtcaacatttcctgttcattattgagca-atcagctgcttgctaacgaaataaagtttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAGAGAAAGTGCTCCTTACAGTTAAGCCACAAT
|| |    |  ||  |||  |||  ||   | | |||   ||| ||| ||  ||| | || || |||||       | | |  | ||||| | ||| || ||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||||||| ||||||||||
gtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaac------tactgtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAGAGAAGGTGCTCCTTACAGTAAAGCCACAAT
















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|58656111|gb|CK044791.1|CK044791
EST:     TGGTACTGTTATATCAGGGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|58677816|gb|CK066503.1|CK066503
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|218486102|gb|FG952697.1|FG952697
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|4880950|gb|AU065249.1|AU065249
EST:     TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29624443|gb|CB629454.1|CB629454
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCA
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCA
EST: gi|29675035|gb|CB671310.1|CB671310
EST:     TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29630489|gb|CB635498.1|CB635498
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29666721|gb|CB662996.1|CB662996
EST:     TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGTAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29626371|gb|CB631382.1|CB631382
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|58682283|gb|CK070970.1|CK070970
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29628610|gb|CB633621.1|CB633621
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttcattattgagcaatcagctgcttgctaacgaaataaagtttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAGAGAAAGTGCTCCTTACAGTTAAGCCACAAT
                            tgctaac  putative branch site (score: 1)
                                    aaataaagttt  TA-rich tract