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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCCATAGGAAGAAGAACTTGCAGTACTATGAGGTGTCAGCTAAGAGCAACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacctcagttatcatcaatctttaattattcagcaacccaattactggattaaaccaactctgttctctgtctttgtcag

Basic information

species Oryza sativa
transcript LOC_Os01g42530.1
intron # 6
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|55442436|gb|CV734536.1|CV734536
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|88291555|gb|CI537341.1|CI537341
EST:     GAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: GAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|87030406|gb|CI252683.1|CI252683
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|29684837|gb|CB681112.1|CB681112
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|58687745|gb|CK076432.1|CK076432
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|38479329|gb|CF963460.1|CF963460
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|218479973|gb|FG945844.1|FG945844
EST:     AACTACNACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGAATGGTAACCTCCAATTTGTGGAAACACCTGCTCTTGCTCC
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGA-TGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCC
EST: gi|88239222|gb|CI240384.1|CI240384
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|58589544|gb|CF987852.1|CF987852
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|88263174|gb|CI366948.1|CI366948
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|86511798|gb|CI154431.1|CI154431
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|11564790|gb|AU165426.1|AU165426
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|88906919|gb|CI375991.1|CI375991
EST:     ATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGGAAACACCTGCTCTTGCTCCTCCAGATG
genomic: ATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGT-GGAAACACCTGCTCTTGCTCCTCCAGATG
EST: gi|88283026|gb|CI404472.1|CI404472
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGGCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|125863363|gb|EL586682.1|EL586682
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|88262960|gb|CI366734.1|CI366734
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|29689309|gb|CB685584.1|CB685584
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|86494370|gb|CI137003.1|CI137003
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|12405389|gb|AU166990.1|AU166990
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|88477395|gb|CI414666.1|CI414666
EST:     ACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: ACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|88260768|gb|CI363061.1|CI363061
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
EST: gi|14980874|gb|BI305552.1|BI305552
EST:     AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGG                         CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT
genomic: AACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGT

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: 72 (upstream exon), 75 (downstream exon)
Score: 37

CCTTCCATAGGAAGAAGAACTTGCAGTACTATGAGGTGTCAGCTAAGAGCAACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacct ... tctttgtcagCGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCCATAGGAAGAAGAACTTGCAGTACTATGAGGTGTCAGCTAAGAGCAACTACAACTTTGAGAAGCCATTCCTGTACCTTGCCAGGAAACTTGCTGGgtaacgacctcagttatcatcaatctttaattattcagcaacccaattactggattaaaccaactctgttctctgtctttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC