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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgctactgcagtatacctacatgctcacttatgtttgtttcttttagataatgtcacttatgtttgtgttttgcataatgttgataatttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCCGGAAAAGGAGCTAGGAGGGGTGGTCTTTTGTTGCAATAACAACACATTC

Basic information

species Oryza sativa
transcript LOC_Os01g07140.2
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|58668320|gb|CK057006.1|CK057006
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88583019|gb|CI699490.1|CI699490
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88588966|gb|CI706813.1|CI706813
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88577141|gb|CI673697.1|CI673697
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88381640|gb|CI682307.1|CI682307
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88582488|gb|CI699903.1|CI699903
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|29633284|gb|CB638293.1|CB638293
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|86904066|gb|CI304500.1|CI304500
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|29633138|gb|CB638147.1|CB638147
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88305805|gb|CI633378.1|CI633378
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88571150|gb|CI662523.1|CI662523
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88449393|gb|CI582265.1|CI582265
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCC-
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88409800|gb|CI571057.1|CI571057
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88576069|gb|CI670214.1|CI670214
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88412659|gb|CI690406.1|CI690406
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88432686|gb|CI690528.1|CI690528
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88585243|gb|CI702860.1|CI702860
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGAATCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88578964|gb|CI687930.1|CI687930
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88347365|gb|CI632650.1|CI632650
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88341488|gb|CI635686.1|CI635686
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88851993|gb|CI679551.1|CI679551
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTCCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88692035|gb|CI735610.1|CI735610
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88302595|gb|CI668441.1|CI668441
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88429131|gb|CI690017.1|CI690017
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88393996|gb|CI684264.1|CI684264
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|88355935|gb|CI653345.1|CI653345
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
EST: gi|58670252|gb|CK058938.1|CK058938
EST:     CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAG                         AATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC
genomic: CAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCC

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: 71 (upstream exon), 49 (downstream exon)
Score: 6

GGTTGATCGATGCTTGCTGCTGCTGCGCGTCGAGGCGGCTCCATCGGCGGCAACCGCTGATCGATCGATCGATCCCGCGGGTTTCGTAGCACCCGAGCAGgtgagcgagc ... tttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCCGGAAAAGGAGCTAGGAGGGGTGGTCTTTTGTTGCAATAACAACACATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagataatgtcacttatgtttgtgttttgcataatgttgataatttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCCGGAAAAGGAGCTAGGAGGGGTGGTCTTTTGTTGCAATAACAACACATTC
                                    tgttgat  putative branch site (score: 6)
                                             tttctc  putative PPT
                                ataatgttgataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctactgcagtatacctacatgctcacttatgtttgtttcttttagataatgtcacttatgtttgtgttttgcataatgttgataatttctcgaagAATGGGTGCTGGAAAGAAGACTCAGACCGAGAACGAGTTCCGTGAGCTCCCGGAAAAGGAGCTAGGAGGGGTGGTCTTTTGTTGCAATAACAACACATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- -tgctact
- - - - - - - - - - tacatgc
- - - - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttga