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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGATCTGGACAACATTTTATTGGAGAATCTCGGTGATGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctttgacaataatctcttttggttctggtggattattttgttaacagaagaaattctcttcag

Basic information

species Oryza sativa
transcript LOC_Os02g44510.1
intron # 7
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|88670211|gb|CI723459.1|CI723459
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATACAGACCCTCCCACGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|58670066|gb|CK058752.1|CK058752
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCCAGGGGTCTTCAGTTTATC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCC-AGGGGTCTTCAGTTTATC
EST: gi|88973721|gb|CI718149.1|CI718149
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGGTCTTCAGTTTATC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGG-TCTTCAGTTTATC
EST: gi|58654435|gb|CK043115.1|CK043115
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAGAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|29629313|gb|CB634324.1|CB634324
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|29624544|gb|CB629555.1|CB629555
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|58695325|gb|CK084012.1|CK084012
EST:     TGTTAGAACATTGCAGGCAG-GTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|88668971|gb|CI719928.1|CI719928
EST:     TGTCAGAACATTGCAGGCAGTGTTTGAACTTGAACCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATACAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|29676303|gb|CB672578.1|CB672578
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|88594071|gb|CI713242.1|CI713242
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|58689586|gb|CK078273.1|CK078273
EST:     GCAG-GTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: GCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
EST: gi|88665626|gb|CI715782.1|CI715782
EST:     TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAG                         GCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC
genomic: TGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCC

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: 20

CCATGATCTGGACAACATTTTATTGGAGAATCTCGGTGATGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctt ... ttctcttcagGCCATTGCAAGGAAAAGGATAGAGACCCTCCCAGGGGTCTTCAGTTTATCCTTGGTACCAAACGAAGACCACACTTGGTAGATACGCTTGTCATGGCCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGATCTGGACAACATTTTATTGGAGAATCTCGGTGATGTTAGAACATTGCAGGCAGTGTTTGAACTTGAAGCACTCCTCTTGACAGgtatagtctttgacaataatctcttttggttctggtggattattttgttaacagaagaaattctcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC