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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattcctgaagctatgtttccatattccacagttagtaatgtgatttgcaaagtattctatctacagttcctaatgtgatttgcaaagtactgatgcatcgccgatctctttgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATCGCCCAGTCTCTCCAGATATACAAGCACATCTGCCAGACCAACAGCTTGA

Basic information

species Oryza sativa
transcript LOC_Os08g06200.1
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|86494336|gb|CI136969.1|CI136969
EST:     TGAGAGTTGCTGAACAATACATGAAGGCATTTGCTAATCTGGCCAAAAAG                         AGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
genomic: TGAGAGTTGCTGAACAATACATGAAGGCATTTGCTAATCTGGCCAAAAAGgtgagattcc ... tgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
EST: gi|25800628|gb|CA756589.1|CA756589
EST:     TGAGAGTTGCTGAACAATACATGAAGGCATTTGCTAATCTGGCCAAAAAG                         AGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
genomic: TGAGAGTTGCTGAACAATACATGAAGGCATTTGCTAATCTGGCCAAAAAGgtgagattcc ... tgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
EST: gi|88218455|gb|CI218304.1|CI218304
EST:     TACATGAAGGCATTTGCTAATCTGGCCAAAAAG                         AGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
genomic: TACATGAAGGCATTTGCTAATCTGGCCAAAAAGgtgagattcc ... tgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
EST: gi|86501223|gb|CI143856.1|CI143856
EST:     TACATGAAGGCATTTGCTAATCTGGCCAAAAAG                         AGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
genomic: TACATGAAGGCATTTGCTAATCTGGCCAAAAAGgtgagattcc ... tgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
EST: gi|88230880|gb|CI228785.1|CI228785
EST:     TTGCTGAACAATACATGAAGGCA-TTGCTAATCTGGCCAAAAAG                         AGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC
genomic: TTGCTGAACAATACATGAAGGCATTTGCTAATCTGGCCAAAAAGgtgagattcc ... tgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATC

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: 60 (upstream exon), 75 (downstream exon)
Score: 23

GCTGCGAACCTGAGAGTTGCTGAACAATACATGAAGGCATTTGCTAATCTGGCCAAAAAGgtgagattcc ... tgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATCGCCCAGTCTCTCCAGATATACAAGCACATCTGCCAGACCAACAGCTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcctaatgtgatttgcaaagtactgatgcatcgccgatctctttgaaacacagAGCAACACGATTCTCCTTCCAAGTGACGCTGGCAACCCATCATCCCTCATCGCCCAGTCTCTCCAGATATACAAGCACATCTGCCAGACCAACAGCTTGA
                      tactgat  putative branch site (score: 23)
                                       tctcttt  putative PPT
                                           tttgaaa  TA-rich tract