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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcctatttctgccacataacaacaggaggaatttgactgccacgagtattattctactttcaattaatacgaatattttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g46580.1
intron # 8
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|89168374|gb|CI109578.1|CI109578
EST:     TGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAA                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: TGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|58685683|gb|CK074370.1|CK074370
EST:     GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAG                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|58685871|gb|CK074558.1|CK074558
EST:     GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAG                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|58678948|gb|CK067635.1|CK067635
EST:     GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAG                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|88247621|gb|CI247470.1|CI247470
EST:     TATACTTTCAAGTCCAA                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: TATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|163928447|gb|EG711347.1|EG711347
EST:     GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAA                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|58603777|gb|CK014305.1|CK014305
EST:     GTGCTGTAGAAGACATTCTTGTCACGATGGGAATATACTTTCAAGTCCAG                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGG
genomic: GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGG
EST: gi|88968869|gb|CI098954.1|CI098954
EST:     CTTTCAAGTCCAA                         GACGATGATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: CTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
EST: gi|58674478|gb|CK063165.1|CK063165
EST:     GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAG                         GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
genomic: GTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG

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), 49 (downstream exon)
Score: 31

GTTGCTTGTGCACTGTTGCTATCTGGAGAGGACTTGACCAAATATGGTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAAgtaactccta ... tttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgactgccacgagtattattctactttcaattaatacgaatattttcttacagGACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG
                              aattaat  putative branch site (score: 31)
                                          tattttctt  putative PPT
               tattattctactttca  TA-rich tract