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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttctacatgtttgtcaagaaagttcatccatgcaatattttctttagtatgttgcaacattcacgctgatcttggtacgctcacttgttataatattgtctattgtgtttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT

Basic information

species Oryza sativa
transcript LOC_Os12g10784.1
intron # 11
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|88258518|gb|CI361104.1|CI361104
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|88505479|gb|CI432985.1|CI432985
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGGGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|88253440|gb|CI352066.1|CI352066
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|163925412|gb|EG711549.1|EG711549
EST:     TACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: TACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|86841827|gb|CI337475.1|CI337475
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|4714258|gb|AU058225.1|AU058225
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|88295502|gb|CI527865.1|CI527865
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|12693436|gb|AU173569.1|AU173569
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|86603000|gb|CI357364.1|CI357364
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGC                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|88836262|gb|CI371367.1|CI371367
EST:     GTACATGATGATCCCTTGGACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|11442603|gb|BF430506.1|BF430506
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|86833012|gb|CI333611.1|CI333611
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|33672946|gb|CF301185.1|CF301185
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCATTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|88473662|gb|CI410933.1|CI410933
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|86526749|gb|CI166955.1|CI166955
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|33688394|gb|CF316633.1|CF316633
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
EST: gi|86839037|gb|CI330405.1|CI330405
EST:     GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG                         CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
genomic: GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT

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), 48 (downstream exon)
Score: 13

GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGgtaaacttct ... tttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgctgatcttggtacgctcacttgttataatattgtctattgtgtttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT
               cgctcac  putative branch site (score: 13)
 tttttgtt  putative PPT
 ttataatattgtctat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttctacatgtttgtcaagaaagttcatccatgcaatattttctttagtatgttgcaacattcacgctgatcttggtacgctcacttgttataatattgtctattgtgtttttgttagCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT