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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttaacaatcatcacgagttccttagcatctttctttactgtttatgccatcttcttacatccgtgaggttcggaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGTTCAGCAGATGGGCAAGCCGGGCATTGAACTCTTCTCGACTTCTGCAAGG

Basic information

species Oryza sativa
transcript LOC_Os02g06910.1
intron # 13
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|25806101|gb|CA762062.1|CA762062
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTGGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|29613687|gb|CB618700.1|CB618700
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|88348079|gb|CI637540.1|CI637540
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|29666700|gb|CB662975.1|CB662975
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|88471175|gb|CI408446.1|CI408446
EST:     GAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCCCAGGAGGT
genomic: GAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|58685183|gb|CK073870.1|CK073870
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|29666699|gb|CB662974.1|CB662974
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|29656950|gb|CB653225.1|CB653225
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
EST: gi|29663501|gb|CB659776.1|CB659776
EST:     TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCA                         GGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT
genomic: TTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGT

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: 74 (upstream exon), 75 (downstream exon)
Score: 13

GCCTTGAGGGCCAGTTGGAAGACCCTTTGAGATCAGGCTGGCAGCTTGTATTTGTTGACCGAGAGGACGACGTTCTTCTAGTTGGCGATGATCCGTGGCAgtaagtttta ... gaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGTTCAGCAGATGGGCAAGCCGGGCATTGAACTCTTCTCGACTTCTGCAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctttactgtttatgccatcttcttacatccgtgaggttcggaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGTTCAGCAGATGGGCAAGCCGGGCATTGAACTCTTCTCGACTTCTGCAAGG
                        ttcttac  putative branch site (score: 13)
           tgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttaacaatcatcacgagttccttagcatctttctttactgtttatgccatcttcttacatccgtgaggttcggaatctgcagGGAATTTGTGAACAGTGTGTCTTGCATAAAGATACTTTCGCCGCAGGAGGTTCAGCAGATGGGCAAGCCGGGCATTGAACTCTTCTCGACTTCTGCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG