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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatttgacattttttcagcttgttcctggatttctgatttcattaactggacttatattgaaacggaattaattacgaacctttgtactccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGT

Basic information

species Oryza sativa
transcript LOC_Os05g02310.1
intron # 1
splice site 3'
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|88381548|gb|CI682205.1|CI682205
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88720264|gb|CI743563.1|CI743563
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|4878573|gb|AU062872.1|AU062872
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88725059|gb|CI748318.1|CI748318
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88351758|gb|CI617483.1|CI617483
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88396360|gb|CI598472.1|CI598472
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|33663512|gb|CF294479.1|CF294479
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|699797|gb|D46088.1|D46088
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|86831354|gb|CI297623.1|CI297623
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88300593|gb|CI587397.1|CI587397
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88400835|gb|CI616840.1|CI616840
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88425227|gb|CI564744.1|CI564744
EST:     CTCGCCTCTTCGTCCCCAGATT-AGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88300279|gb|CI584698.1|CI584698
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|117243396|gb|CT843443.1|CT843443
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|3759881|gb|C97139.1|C97139
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88578597|gb|CI687538.1|CI687538
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
EST: gi|88325992|gb|CI651039.1|CI651039
EST:     CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAG                         GTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA
genomic: CTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCA

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: 75 (upstream exon), 63 (downstream exon)
Score: 65

TCTTCTCTTCTCGTGCCTTCTAGGGTTTCCTCTTCCTCGCACCGCGCCGCCTCGCCTCTTCGTCCCCAGATTCAGATCTACTCCTACTCCTACTACCAAGgtgcgtaact ... tccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactggacttatattgaaacggaattaattacgaacctttgtactccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGT
                                            ctccatc  CT-rich tract
         ttatattgaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatttgacattttttcagcttgttcctggatttctgatttcattaactggacttatattgaaacggaattaattacgaacctttgtactccatcacagGTTGTTGCCATGGCTCCCGCTGTTGAAGCCGTGGAGAAGAAGACAGGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGT

- - - - - - - -ttcagct
- - - - - - - - - - - -gttcctg
- - - - - - - - - - - - - - - - tttctga
- - - - - - - - - - - - - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacggaa