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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATATCGTGCGTATCAAGATACTCAAAAATAAACCAGATCATGCCCTCATCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttggtcacacattcttttattctggacactctcttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtggatgttgctgcgtatcacgctctgttctaatggcatttcctatccag

Basic information

species Oryza sativa
transcript LOC_Os01g64770.2
intron # 14
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|29627974|gb|CB632985.1|CB632985
EST:     TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|88975269|gb|CI023520.1|CI023520
EST:     AGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: AGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|29674457|gb|CB670732.1|CB670732
EST:     TCCAGATGGTTGACGGGCTTCAGGGTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAATTACTCCAAGTACCCA
genomic: TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|88974537|gb|CI022078.1|CI022078
EST:     GGCTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: GGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|4714598|gb|AU055715.1|AU055715
EST:     CCAGATGGCTGACCGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATNCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: CCAGATGGCTGA-CGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|29656749|gb|CB653024.1|CB653024
EST:     TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|29687502|gb|CB683777.1|CB683777
EST:     TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: TCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
EST: gi|58608817|gb|CK036850.1|CK036850
EST:     TTCAGGCTGAGCTTGCTGTACTGTATTTAAAG                         GGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA
genomic: TTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCA

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: 43 (upstream exon), 75 (downstream exon)
Score: 15

GAATATCGTGCGTATCAAGATACTCAAAAATAAACCAGATCATGCCCTCATCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttg ... tcctatccagGGAGCAATGCTATTCGGAAAGAAGCTTGAAGTGAACTACTCCAAGTACCCAACCGTTACTGCTGATCCAGATGCACGTGACTACTCAACTTCTCACCTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATATCGTGCGTATCAAGATACTCAAAAATAAACCAGATCATGCCCTCATCCAGATGGCTGACGGGCTTCAGGCTGAGCTTGCTGTACTGTATTTAAAGgtgcttcttggtcacacattcttttattctggacactctcttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtggatgttgctgcgtatcacgctctgttctaatggcatttcctatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT