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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattcaacctatattaaagaaagaaaatattttagtaaattagtaaatatttattatttataaagcttttcacatgtatgcattaatcttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG

Basic information

species Oryza sativa
transcript LOC_Os02g35130.2
intron # 1
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|163928653|gb|EG710914.1|EG710914
EST:     GTCGCGGGTTCGTCTAAAAGTCCGCAAGATTCGTCGTCGTCCTATCGCCG                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: GTCGCGGGTTCGTCTAAAAGTCCGCAAGATTCGTCGTCGTCCTATCGCCGgtgggtaggg ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88826040|gb|CI776605.1|CI776605
EST:     GTCGCGGGTTCGTCTAAAAGTCCGCAAGATTCGTCGTCGTCCTATCGCCG                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: GTCGCGGGTTCGTCTAAAAGTCCGCAAGATTCGTCGTCGTCCTATCGCCGgtgggtaggg ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG

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: 40 (upstream exon), 36 (downstream exon)
Score: 1

ATTTTTTTTTGTTTTTTAGTTTTTTTTTCTTCTTCGCTTCCTTCGCCGCCGTCGCGGGTTCGTCTAAAAGTCCGCAAGATTCGTCGTCGTCCTATCGCCGgtgggtaggg ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatatttattatttataaagcttttcacatgtatgcattaatcttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG
                                     cattaat  putative branch site (score: 1)
                                           tcttct  CT-rich tract
     atttattatttataaa  TA-rich tract