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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgagctcctcttccccccatggatttgcttcgctgctcgctgccatggcgttgctgcgccgtctcgtgtatgtagcgtattcgctgtttcgagt...

Basic information

species Oryza sativa
transcript LOC_Os07g12250.1
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|88581534|gb|CI698528.1|CI698528
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|325493082|gb|JG457606.1|JG457606
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88348866|gb|CI653910.1|CI653910
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|33670740|gb|CF298979.1|CF298979
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|24468910|gb|CA305859.1|CA305859
EST:     ACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATCGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: ACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88381633|gb|CI682300.1|CI682300
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88348364|gb|CI639023.1|CI639023
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88388417|gb|CI683189.1|CI683189
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88592045|gb|CI710122.1|CI710122
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88571275|gb|CI662648.1|CI662648
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|218483042|gb|FG956499.1|FG956499
EST:     CGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAA-ATGGTTCTCAA
genomic: CGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|86898740|gb|CI296058.1|CI296058
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|3767629|gb|AU031656.1|AU031656
EST:     GGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|55441469|gb|CV734055.1|CV734055
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88763039|gb|CI772595.1|CI772595
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|163927854|gb|EG713502.1|EG713502
EST:     GTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|112787065|gb|EE591987.1|EE591987
EST:     GACGCGGAGGCGCTAGGGTTTTGCCCGCTTCCCACAG                         GTAAGGAGGCATCGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GACGCGGAGGCGCTAGGGTTTTG-CTGC-TCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88290337|gb|CI665126.1|CI665126
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88739146|gb|CI762654.1|CI762654
EST:     GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: GGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
EST: gi|88574546|gb|CI666315.1|CI666315
EST:     AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAG                         GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA
genomic: AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA

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: 39 (upstream exon), 51 (downstream exon)
Score: 62

AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgag ... taatttgcagGTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGAGGCGGACGCGGAGGCGCTAGGGTTTTGCTGCTCCCACAGgtgagtcgagctcctcttccccccatggatttgcttcgctgctcgctgccatggcgttgctgcgccgtctcgtgtatgtagcgtattcgctgtttcgagt

- - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - GCTGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgccg