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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgatactccggcaactcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG

Basic information

species Oryza sativa
transcript LOC_Os10g32880.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G037698_T02 (Zea mays), 3'ss of exon 13
-----gtgtgatactccggcaac---tcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttt-tctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
      | || ||||  || | |   | ||||||| || ||||| |||   |||        |||||| |||| |  |  ||   ||| |  ||| | ||| ||||| ||||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||
gtatgatttggtactatggtatcactttattcaagatcgttttt-aggcagtca--------tgctctcgaaaca--tgactggtaatgacttttctatctgtagTCGAATGTCGCGAAGTTTGAGGGGCATGTAGGACCAGTCACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTAGCG

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G324540_T01 (Zea mays), 3'ss of exon 13
-----gtgtgatactccgg---caactcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttt-tctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
      | || ||||  ||   ||  | ||||||||| | |||| ||||| |||        ||||||| ||| |  |  || | ||| |  ||| | ||| ||||||||||| |||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||
gtgtgatttggtactgtggtgtcactttattcaagtt-tgtttttaggtgatca--------tgctcttaaaacatgt--ctgataatgacatttctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AC205703.4_FGT004 (Zea mays), 3'ss of exon 3
-----gtgtgatactccggcaac--tcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttt-tctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
      | || ||||  ||   |  | ||||||||| | |||| ||||| |||        ||||||| ||| |  |  || | ||| |  ||| | ||| ||||||||| | |||||||||||||| ||||| ||||| || |||| |||||| ||||||||||||||||||||||| |||
gtgtgatttggtactgtggtgtcctttattcaagtt-tgtttttaggtgatca--------tgctcttaaaacatgt--ctgataatgacatttctatctgtagTCAAATATCGCAAAGTTTGAGGGTCATGTCGGACCGGTCACTGTTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G26870.1 (Glycine max), 3'ss of exon 13
gtgtgatactccggcaactcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
              ||| |  |||   | |||| || |    || ||     | | | ||     ||  || || ||  || ||  ||   | ||| |||||||||| | |||||| || |||| ||| ||||| ||||| || || |||||||| ||||| ||||||||||||
---------gtaaacaattt-ttcttatactttgtttaaagtttaattttaatattcact---gttatgtt-cttaccttcctccattggttgtagGCAAATGTTGCTAGGTTTGATGGACATGCTGGGCCAGTAACTGCCATATCTTTCTCTGAGAATGGATACTTCCTTGCG

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 13
--gtgtgatactccggcaactcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
        |  | |    |||  || ||  |    ||| |  | ||||   |||| |  |||  |  | | |     ||  || ||  ||   | ||| |||||||||| | |||||| || |||| ||| ||||| ||||| || || |||||||| ||||| ||||||||||||
gtaaacattttttcttatacttgtttaaagttcaattttaa-tattca---atgt-tattctctatgttctt-----accttcctccattggttgtagGCAAATGTTGCTAGGTTTGACGGACATGCTGGGCCAGTAACTGCCATATCTTTCTCTGAGAATGGATACTTCCTTGCG

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 13
gtgtgatactccggcaactcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
      || |     |  || | ||||||     |    | |||  |  |  |||  | || |  ||  |  ||  |  |  |   ||| |   || ||||||| ||||  ||||| ||||| |||||  | || |||||||| || ||||| |||||||||||||||||||||
-----gtaataaattatgtcttgcaagtttaacct----gggttgttagaattct-ttattcacttatttctctttcttttgttaatttgc---agGCAAATGTGGCAAGATTTGACGGGCACGTTGGGGCTGTAACTGCTATATCTTTCTCAGAAAATGGTTACTTCCTTGCG

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|4879072|gb|AU063371.1|AU063371
EST:     GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAG                         -CAANATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTC
genomic: GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAGgtgtgatact ... ttttctctagTCAA-ATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTC
EST: gi|4879056|gb|AU063355.1|AU063355
EST:     GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAG                         -CAANATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTC
genomic: GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAGgtgtgatact ... ttttctctagTCAA-ATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTC
EST: gi|58686960|gb|CK075647.1|CK075647
EST:     GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAG                         TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCC
genomic: GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAGgtgtgatact ... ttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCC
EST: gi|25797187|gb|CA753148.1|CA753148
EST:     GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAG                         TCAAATGTTGCAAAGTTTGAGGGGCATGTNGGACCAGTGACTGCTATGTCC
genomic: GGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAGgtgtgatact ... ttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 49

ACAAGAGGGATATACATCTGCATCTTTCCACCCAGATGGTCTTATCCTGGGGACAGGGACCACTGAAGCTGTTGTCAAAATTTGGGATGTGAAGACGCAGgtgtgatact ... ttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttttctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG
                             tgctaac  putative branch site (score: 49)
                                      tcatcttttttctct  putative PPT
                                        atctttttt  TA-rich tract