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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattctgattgttagattaagcaaggatttatttgaagcaaatgcgttttaatttcagattaattaacaacagtcatgatctctgttttgttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTCTTGACCAGACGAACATACAAGGAAATGGAGCTCGGCGGCATCAAATATC

Basic information

species Oryza sativa
transcript LOC_Os01g43710.1
intron # 4
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|29620836|gb|CB625847.1|CB625847
EST:     ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|29620926|gb|CB625937.1|CB625937
EST:     ACTTTGAAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|88198907|gb|CI197304.1|CI197304
EST:     CTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: CTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|86505017|gb|CI147650.1|CI147650
EST:     AC-TTGGGAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|88198141|gb|CI197991.1|CI197991
EST:     CTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: CTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|14191810|gb|AU184021.1|AU184021
EST:     ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|25807782|gb|CA763743.1|CA763743
EST:     CTTTGGAAGAACCACACCCAGCCTCTGATAGCCTAAGTCGTCTGAAGATN                         GTACCAATGATCCTGTCCGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: CTTTGGAAGAACCACA-CCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|29620814|gb|CB625825.1|CB625825
EST:     TATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: TATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|29620810|gb|CB625821.1|CB625821
EST:     ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|29620875|gb|CB625886.1|CB625886
EST:     AC-TTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
EST: gi|87037368|gb|CI191990.1|CI191990
EST:     ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATT                         GTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC
genomic: ACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTC

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), 53 (downstream exon)
Score: 18

AAGTATGCACCCAGAGTGGCAAGAGCGAGCAAGAGAAGAAGTGCTACACCACTTTGGAAGAACCACACCAGACTATGATAGCTTAAGTCGTCTGAAGATTgtaagtataa ... gttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTCTTGACCAGACGAACATACAAGGAAATGGAGCTCGGCGGCATCAAATATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttttaatttcagattaattaacaacagtcatgatctctgttttgttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTCTTGACCAGACGAACATACAAGGAAATGGAGCTCGGCGGCATCAAATATC
                 aattaac  putative branch site (score: 18)
                                         ttttgtt  putative PPT
     taatttcagattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattctgattgttagattaagcaaggatttatttgaagcaaatgcgttttaatttcagattaattaacaacagtcatgatctctgttttgttactgcagGTAACAATGATTCTGTACGAGGTTCTTAGGTTGTATCCGCCAGTGGTGTTCTTGACCAGACGAACATACAAGGAAATGGAGCTCGGCGGCATCAAATATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - -ctgattg
- - - - - - - - - - - - - - - - - - - -caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaca