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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcttatccctttgctcaaaatctgaagtcaatagacactgcaattaatccttttggttttgaaagtctaacctactcaaactgtttctgtctcttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGGCTATGACATCAACGACAAGGCTCTTTGCATAGTGGTTCTTATTGCCAAT

Basic information

species Oryza sativa
transcript LOC_Os11g22350.1
intron # 13
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|29675381|gb|CB671656.1|CB671656
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|88966309|gb|CI119444.1|CI119444
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|88259346|gb|CI363639.1|CI363639
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|87029848|gb|CI274529.1|CI274529
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGTAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|88251125|gb|CI349355.1|CI349355
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|88258590|gb|CI361176.1|CI361176
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|86480362|gb|CI122995.1|CI122995
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|87029788|gb|CI274469.1|CI274469
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGTAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|88258120|gb|CI360706.1|CI360706
EST:     GTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: GTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|88255082|gb|CI353906.1|CI353906
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACAGCGGTGCGGTTCGCTGGTCAAGAGCG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACA-CGGTGCGGTTCGCTGGTCAAGAGCG
EST: gi|86837739|gb|CI343219.1|CI343219
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         ATACTCCGGGGTGTGGCTGATTACAC-GTGC-GTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
EST: gi|86479534|gb|CI122167.1|CI122167
EST:     TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAA                         CTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG
genomic: TGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGG

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), 74 (downstream exon)
Score: 16

TTTTGACTCTGATAGCAACTCAGCGGAAGAACACTTTCTTTGCTGACCTGTGCTACACAAAGTGGGCTCTAGAAGGGTTTGTGATGGCAAATGCTCAAAAgtacgtctta ... cttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGGCTATGACATCAACGACAAGGCTCTTTGCATAGTGGTTCTTATTGCCAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttggttttgaaagtctaacctactcaaactgtttctgtctcttgtcgcagCTACTCCGGGGTGTGGCTGATTACACGGTGCGGTTCGCTGGTCAAGAGCGGCTATGACATCAACGACAAGGCTCTTTGCATAGTGGTTCTTATTGCCAAT
                 gtctaac  putative branch site (score: 16)
                                 ctgtttctgtctctt  putative PPT
         ttttgaaa  TA-rich tract