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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattatgcttcactaactttttcatgttatgatgtcactcgatcttaacaaagtggcttcctttttataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGTTCCAACAGCAATGTTTCTGCGAAGTGGTGATATCGTATTGATGGCTGGG

Basic information

species Oryza sativa
transcript LOC_Os11g29690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G844096_T02 (Zea mays), 3'ss of exon 5
--gtaataattatgcttcactaactttttcatg-ttatgatgtcactcgatcttaacaaagtggc--ttcctttttataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGTTCCAACAGCAATGTTTCTGCGAAGTGGTGATATCGTATTGATGGCTGGG
   | ||      |||||  || |||| || || |  | |  ||     | | || |    |  |  ||    |||||   ||||||||||| ||||| ||||| |||||| | ||||| || ||  ||||||||||||||||||||||||| ||||| || |||||||| || ||||||||||||
gtatgatggcccagcttc-ttacctttatcgtgatctttacttcttctaaacatagcgtcttaccagttgtcatttattcttttagTTTGGGCTGCAAATGCATCTTTCTTTTGGGAGGAAAGACTCGAGATGAAGTTCCAACAGCAATGTTCCTGCGCAGCGGTGATATAGTTTTGATGGCTGGG
















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|88981927|gb|CI027505.1|CI027505
EST:     TGTAAGCATAAG                         TTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGT
genomic: TGTAAGCATAAGgtaataatta ... ataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGT
EST: gi|86899515|gb|CI295449.1|CI295449
EST:     CACGTTGATGACATGGAAGCAGATTGGAGTAAACCTATTGTAAGCATAAG                         TTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGT
genomic: CACGTTGATGACATGGAAGCAGATTGGAGTAAACCTATTGTAAGCATAAGgtaataatta ... ataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGT
EST: gi|27546176|gb|CA764490.2|CA764490
EST:     CACGTTGATGACATGGAAGCAGATTGGAGTAAACCTATTGTAAGCATAAG                         TTTGGGGCGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGT
genomic: CACGTTGATGACATGGAAGCAGATTGGAGTAAACCTATTGTAAGCATAAGgtaataatta ... ataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGT

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: 48 (upstream exon), 50 (downstream exon)
Score: 8

GTGACATGCTTGGTGGCCACGTTGATGACATGGAAGCAGATTGGAGTAAACCTATTGTAAGCATAAGgtaataatta ... ataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGTTCCAACAGCAATGTTTCTGCGAAGTGGTGATATCGTATTGATGGCTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgttatgatgtcactcgatcttaacaaagtggcttcctttttataaatttagTTTGGGGTGCAAGTGCATTTTTCTTCTTGGAGGCAAAACGAGAGATGAAGTTCCAACAGCAATGTTTCTGCGAAGTGGTGATATCGTATTGATGGCTGGG
                     tcttaac  putative branch site (score: 8)
                                   cttcctttttat  putative PPT
                                    ttcctttttataaatt  TA-rich tract