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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttttttcagataacaaagttctggcctagtcctgattaaaatatttatacgcgtttcactaatttgaacatctatatttatctctactgactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAATTATCTTGGTGCTATTAAGAATTGGGTTTCACTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g54020.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 2
-----ttttttttttcag---ataacaaagttctggcctagtcctgattaaaatatttatacgcgtttcactaatttgaacatctatatttatctctactgactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAATTATCTTGGTGCTATTAAGAATTGGGTTTCACTTCAG
      || | |  | |    ||   || ||| ||   | || ||||| ||  | ||||  | | |||| ||||   |||||        | | |  ||||  |||||||||||||||||||||||||||||||||||||||| ||| ||||||||||||||||| || || ||||||||||||||| ||||||||
aattagttatataatgaattcatgttaaggttatgatttggttctgataaatctttttactctcttttctctaaaccgaacac-------tgtgttcactg-ttgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATCGGTTCACCTTGGAAATTATCTAGGGGCAATTAAGAATTGGGTTGCACTTCAG

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 2
ttttttttttcagataacaaagttctggcctagtcctgattaaaatatttatacgcgtttcactaatttgaacatctatatttatctctact----gactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAATTATCTTGGTGCTATTAAGAATTGGGTTTCACTTCAG
    |  |      | |  || | | |   ||   |  ||| |  ||||||||    |||     ||| | |  | | |  || |||  |||    |  |||||||| ||  |||| ||||| || |||||||| ||     ||||||| |||||||||||||||||||| || |||||| |  ||||||||
-agatactccaccttgatgaaatacagttttaa--cgaatttatttatttatat-tttttattccattgggatttatgttcttttcttaacttcttgtttgcagGAAGAGGATAGTGTCTGGGGTTCAGCCAACTGGGACTATACACCTAGGAAATTATCTTGGTGCTATAAAAAATTGGATCCCACTTCAG
















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|88341213|gb|CI639970.1|CI639970
EST:     GCTGAAGCGACTGCCTCCGGCGACGAGGCGCCTGCTCCTCCGGCTAGGAA                         GAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAA
genomic: GCTGAAGCGACTGCCTCCGGCGACGAGGCGCCTGCTCCTCCGGCTAGGAAgtaagcccct ... ctgactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAA
EST: gi|88341927|gb|CI644264.1|CI644264
EST:     GCTGAAGCGACTGCCTCCGGCGACGAGGCGCCTGCTCCTCCGGCTAGGAA                         GAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAA
genomic: GCTGAAGCGACTGCCTCCGGCGACGAGGCGCCTGCTCCTCCGGCTAGGAAgtaagcccct ... ctgactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAA
EST: gi|88335142|gb|CI658149.1|CI658149
EST:     GCTGAAGCGACTGCCTCCGGCGACGAGGCGCCTGCTCCTCCGGCTAGGAA                         GAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAA
genomic: GCTGAAGCGACTGCCTCCGGCGACGAGGCGCCTGCTCCTCCGGCTAGGAAgtaagcccct ... ctgactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatacgcgtttcactaatttgaacatctatatttatctctactgactgcagGAAAAGAGTAGTTTCTGGTGTACAGCCAACAGGATTGGTACACCTTGGAAATTATCTTGGTGCTATTAAGAATTGGGTTTCACTTCAG
                                           tactgac  putative branch site (score: 1)
                                       tctctact  CT-rich tract
                  taatttgaacatctat  TA-rich tract