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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactccttccatatgcatgcttaattagcctcagcccaaatattatactattgatgatgaatggaacacacactgtgtgagtgggtctgtctgtctgtgcatgtttgtatttgcactagatcgattatataaacctgctgatacggtaataataataataatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g01150.2
intron # 10
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|38477990|gb|CF962123.1|CF962123
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
EST: gi|58590997|gb|CF989305.1|CF989305
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
EST: gi|117233241|gb|CT848054.1|CT848054
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
EST: gi|11442863|gb|BF430762.1|BF430762
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCCGGTTTGGGGGAACCCGAATCTAGTGGAGCC
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCC-GGTTTGGGGGAACCCGAATCTAGTGGAGCC
EST: gi|38471467|gb|CF955598.1|CF955598
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
EST: gi|58605093|gb|CK033126.1|CK033126
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
EST: gi|24468876|gb|CA305825.1|CA305825
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
EST: gi|58593170|gb|CF991478.1|CF991478
EST:     TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTT                         GGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA
genomic: TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCA

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: 75 (upstream exon), 71 (downstream exon)
Score: 28

TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactc ... aataatgcagGGCAAGATCAAGGGTTATCCGGTTTGGGGGAACCCGAATCTAGTGGAGCCATTTCTCAAGGAGGATGCAACGCCGCCAGCTGCTTGCCCCAGCATTGTTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACGCGCGAAGGAATGGCAACACTTGCTGCTCTAAACGTTCTTgtaagtactccttccatatgcatgcttaattagcctcagcccaaatattatactattgatgatgaatggaacacacactgtgtgagtgggtctgtctgtctgtgcatgtttgtatttgcactagatcgattatataaacctgctgatacggtaataataataataatgcag

- - - - - AAGGAA
- - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - -  GCTGCT