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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttacaccgacattcaaattttttcgaacacaaatatttaggctaaaggtctttattgttctttctttgaag

Basic information

species Oryza sativa
transcript LOC_Os12g10784.1
intron # 12
splice site 5'
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:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCTCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88505479|gb|CI432985.1|CI432985
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGGGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88253440|gb|CI352066.1|CI352066
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|163925412|gb|EG711549.1|EG711549
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86841827|gb|CI337475.1|CI337475
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|4714258|gb|AU058225.1|AU058225
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88295502|gb|CI527865.1|CI527865
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|12693436|gb|AU173569.1|AU173569
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86603000|gb|CI357364.1|CI357364
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAACCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88836262|gb|CI371367.1|CI371367
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAACCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|11442603|gb|BF430506.1|BF430506
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86833012|gb|CI333611.1|CI333611
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|33672946|gb|CF301185.1|CF301185
EST:     CCATTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88473662|gb|CI410933.1|CI410933
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86526749|gb|CI166955.1|CI166955
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCGCCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|33688394|gb|CF316633.1|CF316633
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|7404274|gb|AU066118.2|AU066118
EST:     GGCCA-TGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCNAA
genomic: GGCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86839037|gb|CI330405.1|CI330405
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA

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), 73 (downstream exon)
Score: 21

CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAAGAATAATCTGGTCCAGTTGGTAGGAAATAATGGGCACACTTGCTTGGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttacaccgacattcaaattttttcgaacacaaatatttaggctaaaggtctttattgttctttctttgaag

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