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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctgtctattctgtccaaactatttgagatgatagaacatgttgcatcgttgccctcagatggtttgctgactgttaatattttcctgaaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATTTGTCTCAACAATCTCATGTTTCAAACCAGTGGACACCTGAGCAGCTGCC

Basic information

species Oryza sativa
transcript LOC_Os03g26970.1
intron # 10
splice site 3'
intron type U2

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|27548112|gb|CA766216.2|CA766216
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88265048|gb|CI368822.1|CI368822
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTC-A                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|33654276|gb|CF276890.1|CF276890
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88487839|gb|CI425110.1|CI425110
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88966724|gb|CI365947.1|CI365947
EST:     TCCGCCAACAACATTGAAA-GGGGATAATCCGATCGGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|55408396|gb|CV720772.1|CV720772
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88239397|gb|CI240559.1|CI240559
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|58031158|gb|CX728701.1|CX728701
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88238655|gb|CI238504.1|CI238504
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88238554|gb|CI238403.1|CI238403
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|89193863|gb|CI018181.1|CI018181
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88510139|gb|CI437645.1|CI437645
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88205175|gb|CI205024.1|CI205024
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|66923272|gb|CX110120.1|CX110120
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88199790|gb|CI199640.1|CI199640
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88252854|gb|CI350279.1|CI350279
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88460463|gb|CI531936.1|CI531936
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88205583|gb|CI205432.1|CI205432
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88491702|gb|CI428974.1|CI428974
EST:     TCCCCCCACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|163918128|gb|EG713166.1|EG713166
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|33691029|gb|CF319268.1|CF319268
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88222631|gb|CI222587.1|CI222587
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88476085|gb|CI413356.1|CI413356
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88215513|gb|CI215362.1|CI215362
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|88289738|gb|CI525070.1|CI525070
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|11233514|gb|AU164926.1|AU164926
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGNTCTGAGCCCTGCAGAGATCAAGGNTTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|86512001|gb|CI154634.1|CI154634
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|33808226|gb|CF330002.1|CF330002
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTTTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
EST: gi|8859749|gb|AU097067.1|AU097067
EST:     TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAA                         GGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT
genomic: TCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATT

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: 66 (upstream exon), 75 (downstream exon)
Score: 61

ATATGAAGGACAAATCTCCGCCAACAACATTGAAATTGGGATAATCCGATCTGACCGTGAATTCAAgtatgataca ... aaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATTTGTCTCAACAATCTCATGTTTCAAACCAGTGGACACCTGAGCAGCTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcgttgccctcagatggtttgctgactgttaatattttcctgaaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATTTGTCTCAACAATCTCATGTTTCAAACCAGTGGACACCTGAGCAGCTGCC
                               ttaatattttcctgaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctgtctattctgtccaaactatttgagatgatagaacatgttgcatcgttgccctcagatggtttgctgactgttaatattttcctgaaaaatacagGGTTCTGAGCCCTGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAATAATTTGTCTCAACAATCTCATGTTTCAAACCAGTGGACACCTGAGCAGCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - tattctg
- - - - - - - - - - - - - - -gatgata
- - - - - - - - - - - - - - - - - - - - atgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac