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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaagttccatccatgcaaaatctgatgttatatgcactttatagtccttacacagttatcttttgtag

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
intron # 5
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|2443060|gb|C74831.1|C74831
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGT
EST: gi|701729|gb|D48020.1|D48020
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|86413547|gb|CI019132.1|CI019132
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29655936|gb|CB652211.1|CB652211
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|55410639|gb|CV723015.1|CV723015
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|58691812|gb|CK080499.1|CK080499
EST:     TTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: TTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29616466|gb|CB621478.1|CB621478
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|28298176|gb|CB238406.1|CB238406
EST:     CAATATCTGGTGCTGGCCGTTTCCTGCAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAGAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29663371|gb|CB659646.1|CB659646
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29687246|gb|CB683521.1|CB683521
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|163927355|gb|EG710663.1|EG710663
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|84117136|gb|CD150903.1|CD150903
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|33801701|gb|CF326722.1|CF326722
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|38480498|gb|CF964587.1|CF964587
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29655935|gb|CB652210.1|CB652210
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29672976|gb|CB669251.1|CB669251
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29677863|gb|CB674138.1|CB674138
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|87008043|gb|CI297021.1|CI297021
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|58690422|gb|CK079109.1|CK079109
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29616196|gb|CB621208.1|CB621208
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29644300|gb|CB649307.1|CB649307
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|13420475|gb|AU174565.1|AU174565
EST:     CAATATCTGGNGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTNGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|300215770|gb|HO088396.1|HO088396
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|29684900|gb|CB681175.1|CB681175
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCT
EST: gi|38478600|gb|CF962733.1|CF962733
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         T
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtag-
EST: gi|38478600|gb|CF962733.1|CF962733
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         T
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtag-
EST: gi|38481934|gb|CF965999.1|CF965999
EST:     CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAG                         GTTATTGGTATTGAGCCTTCTG
genomic: CAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTG

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), 71 (downstream exon)
Score: 223

TTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaa ... tcttttgtagGTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTGCTGGCCGTTTCCTGAAAGAGAAAAATCCTGGAATTAAGgtttctttaagttccatccatgcaaaatctgatgttatatgcactttatagtccttacacagttatcttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA