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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggaaatgttagaatgacttacattgtgaaacggagggagtaataactaacaaaattaaccataatctgattcgctgatcaattgactccggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG

Basic information

species Oryza sativa
transcript LOC_Os01g65880.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65880.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G12740.1 (Glycine max), 3'ss of exon 4
tgggaaatgttagaatgacttacattgtgaaa-cggagggagtaataactaa-caaaattaaccataa-tctgattcgctgatcaattgactccggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG
    | ||    ||  |    |  |    |||  |  || | || ||  |   ||| ||| |   |   ||||| |   |  |  |||     |  ||||||||| || |||||||| || ||||| |||||||||||||| ||| |  | || ||||  ||||| || || ||||| |||||||| ||||  || ||||| |
---tacatagctgagaggtcaatgtaaaaaaaatgttggtaatactagttgttcaagattcagagtgggtctgagtttattgtggatttgaaactctgtgcagAGACTAGTGATCAAAACTAAGAGTGTGGAGTTCATGCCCTTCTTCTTGTCGCTGTTTGTGTTTCTCTGTGGCACTTCCTGGTTTATCTTTGGTCTGCTAG

upper sequence: LOC_Os01g65880.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G27610.1 (Glycine max), 3'ss of exon 4
tgggaa--atgttagaatgacttacattgtgaaacggagggagtaataactaacaaaattaaccataatctgattcgctgatcaattgactccggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG
| | ||  |||||  ||| |  | |        |  |    | |   || | | | | ||  | |||   |  |||  |  |  |  |  |  | |||||||||||| |||||||| || |||||||||||||||||||| ||| | ||||| || |  |||||||| || || || || |||||||||||||| || || |
tagaaagtatgttgcaattatattccaaacattattgtataaattccaagtgagatatttttctatagattc-ttcattattttagagtgtgtg-tgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG

upper sequence: LOC_Os01g65880.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G09140.1 (Glycine max), 3'ss of exon 4
tgggaaatgttagaatg--acttacattgtgaaacggagggagtaataactaacaaaattaaccataatctgattcgctgatcaa--ttgactccg-gtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG
      |||||  |||   | |   |   |   |       | |   |  | | | | ||   ||||   |  || | |  | ||  ||| |   | || |||||||||| ||||| || || |||||||||||||||||||| ||| | ||||| || |  |||||||| || ||||| || |||||||||||||| || || |
-----tatgttgcaatcttattccaaacatattattatataaatttcatatgagatatttttgcatagatttttttgttagtgaactttggcattgtgtatgcagAGGCTAGTGATAAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGCACATCTTGGTTCATCTACGGGCTACTAG

upper sequence: LOC_Os01g65880.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G42040.1 (Glycine max), 3'ss of exon 4
-tgggaaatgttagaatgacttacattgtgaaacggagggagtaataact-aacaaaattaaccataatctgattcgctgatcaattgactccggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG
  || | |      |   |       |       ||    | || ||  | ||||   |||       | || ||   ||   | ||||  |   ||||||||| || |||||||| || ||||| |||||||||||||| ||| |  | || ||||  || || || |||||||| |||||||| ||||  || ||||| |
caggaacactacctaggaaaccgtgctagttgttggtaatactagtagttcaacattcttagtgggtgtgtg-ttaattgtggatttgaaacta-tgtgcagAGACTAGTGATCAAAACCAAGAGTGTGGAGTTCATGCCCTTCTTCTTGTCTCTGTTTGTTTTTCTCTGCGGCACTTCCTGGTTTATCTTTGGTCTGCTAG

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|58673060|gb|CK061746.1|CK061746
EST:     CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATG                         AGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
genomic: CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATGgtaagacagt ... cggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
EST: gi|11172087|gb|AU164110.1|AU164110
EST:     CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATG                         AGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
genomic: CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATGgtaagacagt ... cggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
EST: gi|11026129|gb|AU162730.1|AU162730
EST:     CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATG                         AGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
genomic: CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATGgtaagacagt ... cggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
EST: gi|8856858|gb|AU094176.1|AU094176
EST:     CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATG                         AGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
genomic: CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATGgtaagacagt ... cggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
EST: gi|58674455|gb|CK063141.1|CK063141
EST:     CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATG                         AGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC
genomic: CCGCCACCATCTTCTCCATCTGCATGTACGCCTCGCCTCTCTCCATCATGgtaagacagt ... cggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactaacaaaattaaccataatctgattcgctgatcaattgactccggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG
       aaaattaaccataat  TA-rich tract