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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattagttatgtagcaccgaaatttcacgatcttattttcattctatttatttgtttgcaccgaaattaccttttgtttattattcattccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGTACAAGGAGCAAATTGCGTTGACCAAGATACCTGTAACTCTTCTGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os12g02094.1
intron # 2
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|88445523|gb|CI587136.1|CI587136
EST:     CTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATG
genomic: CTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTT-Ggtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATG
EST: gi|112786000|gb|EE591849.1|EE591849
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTTATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|33799287|gb|CF325500.1|CF325500
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|33682433|gb|CF310672.1|CF310672
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|218503573|gb|FG955591.1|FG955591
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88689898|gb|CI733977.1|CI733977
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88425446|gb|CI567166.1|CI567166
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88689967|gb|CI734046.1|CI734046
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|33685697|gb|CF313936.1|CF313936
EST:     CAGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAAGGNATTTTG                         TTGTCCTTGATCTAGAAACAACTGAGGTCGNGGGAAGATGCTAGCCCAAT
genomic: CTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATG-ATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCG-GGGAAGATGCTAGCCCAAT
EST: gi|88689163|gb|CI732739.1|CI732739
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88688761|gb|CI732337.1|CI732337
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88311321|gb|CI570395.1|CI570395
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88302529|gb|CI668375.1|CI668375
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|33662366|gb|CF293333.1|CF293333
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|33674096|gb|CF302335.1|CF302335
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|3759063|gb|C96762.1|C96762
EST:     CCTGTTAATCGTCACCTGCGGAG-TGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88691138|gb|CI735217.1|CI735217
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|86596763|gb|CI286676.1|CI286676
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88689486|gb|CI733062.1|CI733062
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88691293|gb|CI733877.1|CI733877
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88335964|gb|CI645565.1|CI645565
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88403184|gb|CI570925.1|CI570925
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88329157|gb|CI657232.1|CI657232
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88690026|gb|CI734105.1|CI734105
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88691778|gb|CI733355.1|CI733355
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88363793|gb|CI610553.1|CI610553
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88312110|gb|CI580275.1|CI580275
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88688631|gb|CI732207.1|CI732207
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
EST: gi|88396817|gb|CI577966.1|CI577966
EST:     CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTG                         TTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT
genomic: CCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGT

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: 72 (upstream exon), 74 (downstream exon)
Score: 48

TGCAGCCAGAAAGAGGCGATGGATTTCAAAGTCGCTTCCTTTCTCCTACTCCTGTTAATCGTCACCTGCGGAGCTGCTCAAGGTCAAGGCAATGATTTTGgtacgcccta ... tccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGTACAAGGAGCAAATTGCGTTGACCAAGATACCTGTAACTCTTCTGAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttatttgtttgcaccgaaattaccttttgtttattattcattccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGTACAAGGAGCAAATTGCGTTGACCAAGATACCTGTAACTCTTCTGAGGAG
                          ccttttgtttattatt  CT-rich tract
                    aaattaccttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattagttatgtagcaccgaaatttcacgatcttattttcattctatttatttgtttgcaccgaaattaccttttgtttattattcattccttctcagTTGTCCTTGATCTAAAAACAACTGAGGTCGGGGAAGATGCTAGCCCAATGTACAAGGAGCAAATTGCGTTGACCAAGATACCTGTAACTCTTCTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - -tgtagca
- - - - - - - - -accgaaa
- - - - - - - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc