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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTCTGCCACCGCTCGTCTTCCTCCCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcccgctcgctcgctcgctctctcgatccccattccggcaagcgttcgcctctgcttccccaccgcgcgtgccggcgccgtagtttctcgacc...

Basic information

species Oryza sativa
transcript LOC_Os03g37970.1
intron # 1
splice site 5'
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|4878731|gb|AU063030.1|AU063030
EST:     CGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: CGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|218497465|gb|FG944659.1|FG944659
EST:     CGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: CGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|88675804|gb|CI729376.1|CI729376
EST:     CCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGNCGCGCAG                         GTAACAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|38471417|gb|CF955548.1|CF955548
EST:     CGCTCTCCTCTTCGCTCCGCCGCGCAG                         GTCAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: CGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|218479989|gb|FG966405.1|FG966405
EST:     CGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: CGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|58675597|gb|CK064284.1|CK064284
EST:     GCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: GCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|88313010|gb|CI592294.1|CI592294
EST:     CCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCAGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: CCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|58684746|gb|CK073433.1|CK073433
EST:     TTCGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: TTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|58695028|gb|CK083715.1|CK083715
EST:     TCGCTCTCCTCTTCGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: TCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|218482999|gb|FG956127.1|FG956127
EST:     CCTCTTCGCTCCGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: CCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
EST: gi|58586914|gb|CF985222.1|CF985222
EST:     TCGCTCATCCTCTTCGGTCGGCCGCGCAG                         GTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA
genomic: TCGCTC-TCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAA

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: 88

CCCCTCTGCCACCGCTCGTCTTCCTCCCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcc ... atgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAATGGCCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCTCTGCCACCGCTCGTCTTCCTCCCACCTTCCGCCGCCGCCGCCGTCGCTCTCCTCTTCGCTCCGCCGCGCAGgtacgccgcccgctcgctcgctcgctctctcgatccccattccggcaagcgttcgcctctgcttccccaccgcgcgtgccggcgccgtagtttctcgacc

- - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccggcg