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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaatcctcttataatctggcatgcattctttctatatatatggaacaactacctgtccagttttgctcatggaattgaagggagactacatgtcactcttgaccatgctaccaactgtttgtacactgacgtggatagcaatttgatgttgcgacag

Basic information

species Oryza sativa
transcript LOC_Os01g10290.2
intron # 9
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|29638207|gb|CB643216.1|CB643216
EST:     CCTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88830849|gb|CI079283.1|CI079283
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88226114|gb|CI226030.1|CI226030
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|86870218|gb|CI319324.1|CI319324
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|89194317|gb|CI116754.1|CI116754
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|86838969|gb|CI330376.1|CI330376
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88220871|gb|CI218722.1|CI218722
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88290160|gb|CI550382.1|CI550382
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|86889035|gb|CI314651.1|CI314651
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|86488895|gb|CI131528.1|CI131528
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|86497450|gb|CI140083.1|CI140083
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88550813|gb|CI480811.1|CI480811
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|29686213|gb|CB682488.1|CB682488
EST:     ACTATGGACTTCGATTTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|87015628|gb|CI277586.1|CI277586
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88323392|gb|CI553637.1|CI553637
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
EST: gi|88489074|gb|CI426345.1|CI426345
EST:     ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAG                         GAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA
genomic: ACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCA

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: 64 (upstream exon), 58 (downstream exon)
Score: 3

TATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaa ... gttgcgacagGAAAGGGAAAGATCCTGTAGAAGGTGTACCAAGGCTTATCATGGTGCCCCAAATAATCATTGCTTGTTGGAAAGAATTGTATATGCAATATGTGCGTGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTTGTTAATTGAAGgtatgcacaatcctcttataatctggcatgcattctttctatatatatggaacaactacctgtccagttttgctcatggaattgaagggagactacatgtcactcttgaccatgctaccaactgtttgtacactgacgtggatagcaatttgatgttgcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG