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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTCCCGGACGTCTCCTCGGCGAGTTCGCCCGCCGCCTCGCCTGCGTCGATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatccatctgttacgcgcatcctctttctcatctctctctagccacacttttacttgcgttagccgttagccctaccttcacttcacttctaga...

Basic information

species Oryza sativa
transcript LOC_Os04g48770.1
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|88343864|gb|CI654900.1|CI654900
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88315253|gb|CI611917.1|CI611917
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88722801|gb|CI746311.1|CI746311
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88386212|gb|CI572829.1|CI572829
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88407442|gb|CI586283.1|CI586283
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATGTT
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATGTT
EST: gi|88368046|gb|CI572767.1|CI572767
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88312012|gb|CI580177.1|CI580177
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88386211|gb|CI572828.1|CI572828
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88361848|gb|CI682012.1|CI682012
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88393733|gb|CI621228.1|CI621228
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|58588357|gb|CF986665.1|CF986665
EST:     ATCTCCATCGCCGCGGGGGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88738677|gb|CI762185.1|CI762185
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88582268|gb|CI699664.1|CI699664
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGNAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|58595974|gb|CK006502.1|CK006502
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88359976|gb|CI679746.1|CI679746
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGAACTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88335570|gb|CI642794.1|CI642794
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88314800|gb|CI608259.1|CI608259
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88349807|gb|CI634342.1|CI634342
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|88330242|gb|CI658551.1|CI658551
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|58689043|gb|CK077730.1|CK077730
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
EST: gi|14191699|gb|AU183910.1|AU183910
EST:     ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTG                         GTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG
genomic: ATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG

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: 55 (upstream exon), 45 (downstream exon)
Score: 3

GACTCCCGGACGTCTCCTCGGCGAGTTCGCCCGCCGCCTCGCCTGCGTCGATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatc ... tccttcgtagGTTACGAGCCTGGGAGAAGTTGAGGCAAAGACCTGCAGCAAAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTCCCGGACGTCTCCTCGGCGAGTTCGCCCGCCGCCTCGCCTGCGTCGATCTCCATCGCCGCCGGCGTCTGCTGCTTCCGCCGCATCCTCGCTCGCTGgtgagcaatccatctgttacgcgcatcctctttctcatctctctctagccacacttttacttgcgttagccgttagccctaccttcacttcacttctaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctacc