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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttataaaacagttgtcgttctttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

Basic information

species Oryza sativa
transcript LOC_Os01g40840.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 4
tgcttataaaacagt--tgtcgttctttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
  | | ||  | |||  | | |||||| |||| | ||||||  |  ||||||  |||||| ||| ||| | ||| ||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
--cctgtagtatagtctttttgttcttcgctcgtgaaggttccctcatatggtcacaaattaaaaatattctttattcaatggatatcaatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
-tgcttataaaacagttgtcgttctttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
 ||    |||||   || | ||||||  ||||| ||||||  |  ||||||   |||||  || |||   ||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
ttgacagtaaaatcatt-ttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 4
tgcttataaaacagttgtcgttctttgctcataaaggttt-----gccgatatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
    ||    |  ||| |  |  | ||  |||   |||||        ||| ||  ||| || || | | |  ||   ||||||| || |  ||||| || |||||| |||||||||||||| |||||||| | |||||||||||||||||||| ||||   || ||||||||||| ||||| ||||| |||||||| || || |
--tatagtggattgtttttata-tatgtccatgtgggttttattcatggatttgataactaagcagaaaca--ttcctttcaatgcattttaatggtgttatcagGTCTTTGAGAAGCTTGGACCAAGCTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTCCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
tgcttataaaacagttgtcgttc-tttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttct-tcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
 |  ||||       ||| |||  ||| |||||   | |||         |     ||  |||   ||  || || | |||| |     |||||  |  ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| ||||    | || ||| |||  ||||| ||||| |||||| | || || |
cgtgtatagtgtttgtgtagtttgtttactcatgtggatttttt--cgaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 5
tgcttataaaacagttgtcgttctttgctcataaagg--tttgccgata----tggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
      |   | ||||    ||  || |||     ||  ||     |||    |||||||  | ||  || |  ||   || |||| |  |  ||||| ||  ||||| |||||||||||||| ||||| || | |||||||||||||||||||| ||||   || || |||||||| ||||| ||||| |||||||| || || |
------tgtgatagtttgaattaatttctccctgtggacttcattcataagactggaaacttaacattgaaatcttcctttgaatgcactttaatggtgttaccagGTGTTTGAGAAGCTTGGACCAAGTTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTTCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
                                              ttttgtc  CT-rich tract
     aaacaaatcaaagata  TA-rich tract