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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTCGTCGGCTCCTCTGACAAACCCCAGCAGGAGTACGGCACCGCCCTCCCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatccatcggccccgcacctgttcgttttatacattctcctcccttccacgcgctgatcgtgctagtgctcgtgctcgtgcccag

Basic information

species Oryza sativa
transcript LOC_Os01g72650.1
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|88315637|gb|CI615509.1|CI615509
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|58662600|gb|CK051286.1|CK051286
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88305463|gb|CI630625.1|CI630625
EST:     CGCCCGCT-CGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CGCCCG-TCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88337451|gb|CI630748.1|CI630748
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88315936|gb|CI618812.1|CI618812
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88347090|gb|CI631170.1|CI631170
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCNT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGC-T
EST: gi|88582438|gb|CI699851.1|CI699851
EST:     CCGCCCGTCCGTCGCCGGNGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88372401|gb|CI619731.1|CI619731
EST:     CCGCCCGTCCGTCGCCGACGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88345614|gb|CI629875.1|CI629875
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTNGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGNGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88353355|gb|CI631540.1|CI631540
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88337722|gb|CI632224.1|CI632224
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88353396|gb|CI631581.1|CI631581
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         NCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88587934|gb|CI705716.1|CI705716
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|66923971|gb|CX110819.1|CX110819
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88305629|gb|CI631996.1|CI631996
EST:     CGCCCNGTC-GTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGNGGGCTT
genomic: CGCCC-GTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88348771|gb|CI631465.1|CI631465
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT
EST: gi|88353381|gb|CI631566.1|CI631566
EST:     CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAG                         CCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCT-CCCGGCGGGCTT
genomic: CCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTT

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: 10 (upstream exon), 66 (downstream exon)
Score: 1

CCCTCGTCGGCTCCTCTGACAAACCCCAGCAGGAGTACGGCACCGCCCTCCCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatcca ... tcgtgcccagCCCATCTCGGGTAGGAGGAGCTCAGCGCCGTCGACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTCGTCGGCTCCTCTGACAAACCCCAGCAGGAGTACGGCACCGCCCTCCCGCCCGTCCGTCGCCGGCGAAACTAGGTCGTAACTTCCCAGCCGAGCAGgtgagatccatcggccccgcacctgttcgttttatacattctcctcccttccacgcgctgatcgtgctagtgctcgtgctcgtgcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG