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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattgattcaaagcattagctggaattctttagtctaacgattgaaaatcattaattttacttccagtttgttacttattggctgttttactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCTGCTGTTTCAAGTAGCCGAGATGTGATGCCTATTGATACTTCTGAACCAT

Basic information

species Oryza sativa
transcript LOC_Os01g51200.2
intron # 12
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|58603326|gb|CK013854.1|CK013854
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGCAGGCC
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGG-AGGCC
EST: gi|27554289|gb|CA998189.1|CA998189
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
EST: gi|286924|gb|D15731.1|D15731
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGT-                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
EST: gi|88837421|gb|CI078781.1|CI078781
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
EST: gi|58663205|gb|CK051891.1|CK051891
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
EST: gi|4714842|gb|AU055959.1|AU055959
EST:     TCTAAAGANCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: TCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
EST: gi|58682068|gb|CK070755.1|CK070755
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
EST: gi|58672736|gb|CK061422.1|CK061422
EST:     AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTG                         ATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT
genomic: AACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCT

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: 73 (upstream exon), 75 (downstream exon)
Score: 41

GGATCGGCGCCGTGCCCCACCCCCTATTGCAAGTGTTGGGACTTTGGCTAAACAGAAGGCACCTGTGGGAAATGATGCTTCTTTTTCTAAAGAGCCCGTGgtgagttagt ... tactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCTGCTGTTTCAAGTAGCCGAGATGTGATGCCTATTGATACTTCTGAACCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaatcattaattttacttccagtttgttacttattggctgttttactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCTGCTGTTTCAAGTAGCCGAGATGTGATGCCTATTGATACTTCTGAACCAT
      cattaat  putative branch site (score: 41)
                                       ctgtttt  putative PPT
     tcattaattttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtattgattcaaagcattagctggaattctttagtctaacgattgaaaatcattaattttacttccagtttgttacttattggctgttttactatttagATATCTGCCTCGAATTTTTTGGGACGATCTAGTGGATCTTCAAGGAGGCCTGCTGTTTCAAGTAGCCGAGATGTGATGCCTATTGATACTTCTGAACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG