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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcattttacctcagaatcattcttcctgtctgtttgctctgttagagccgatcctcttaaatatcataatgcacctagaatgaatcttaggagtg...

Basic information

species Oryza sativa
transcript LOC_Os04g42010.1
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|86429750|gb|CI082173.1|CI082173
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACCATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88843313|gb|CI372213.1|CI372213
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCC
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|33798570|gb|CF325143.1|CF325143
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86871953|gb|CI332125.1|CI332125
EST:     ATAAAGGCCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGTTCC
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88993134|gb|CI108762.1|CI108762
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|89197113|gb|CI021953.1|CI021953
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|89193612|gb|CI116245.1|CI116245
EST:     ATAAAGGTCGTTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86431392|gb|CI085003.1|CI085003
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86862127|gb|CI330697.1|CI330697
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86603303|gb|CI112063.1|CI112063
EST:     ATAAAGGCCGGTCAAGGAAAATATAGAGACNATAGAAGTAACAGGGGAAG                         GGACTGGAAGGATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88256528|gb|CI358916.1|CI358916
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86427996|gb|CI073093.1|CI073093
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88907105|gb|CI089899.1|CI089899
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86432658|gb|CI086269.1|CI086269
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86430286|gb|CI082709.1|CI082709
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88518308|gb|CI445962.1|CI445962
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88837163|gb|CI078523.1|CI078523
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86430372|gb|CI082795.1|CI082795
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACTATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGTCGTGGTC
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAG-CGTGGTC
EST: gi|88376216|gb|CI533118.1|CI533118
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|89192806|gb|CI050104.1|CI050104
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|33799670|gb|CF325698.1|CF325698
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86842260|gb|CI335194.1|CI335194
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCC
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88218676|gb|CI218525.1|CI218525
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATTACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|86425885|gb|CI070982.1|CI070982
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|218478715|gb|FG955118.1|FG955118
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
EST: gi|88837171|gb|CI078531.1|CI078531
EST:     ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG                         GGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG
genomic: ATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCG

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), 52 (downstream exon)
Score: 8

GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcatt ... acttttctagGGACTGGAAGAATAACAGGGGCGGGAGGCACTTCGGTGGGAAGCGTGGTCGCCACTCGGACGGCCATGAAAGGGCAAATAAAGCTCGAAAAGTCGATGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAGgtatttcattttacctcagaatcattcttcctgtctgtttgctctgttagagccgatcctcttaaatatcataatgcacctagaatgaatcttaggagtg

- - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT