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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatttataggattaaaaatttcttgtttcctgtgctcgaaattgccaggctcgaaaatttctgtctgttctgaaaccaggcaatctttttgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGTATGAGC

Basic information

species Oryza sativa
transcript LOC_Os01g42530.1
intron # 2
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|88733555|gb|CI756732.1|CI756732
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|218479973|gb|FG945844.1|FG945844
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTC-TCGTTGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88329358|gb|CI653273.1|CI653273
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88326643|gb|CI658364.1|CI658364
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGGACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88825209|gb|CI775774.1|CI775774
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88696329|gb|CI739904.1|CI739904
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|2311042|gb|C27197.1|C27197
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88346234|gb|CI634107.1|CI634107
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88352570|gb|CI654395.1|CI654395
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|25802747|gb|CA758708.1|CA758708
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|56158064|gb|C72115.2|C72115
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|428684|gb|D24836.1|D24836
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88720998|gb|CI744297.1|CI744297
EST:     GTGGACTNA-CCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GTGGACT-ACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|88290672|gb|CI667045.1|CI667045
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
EST: gi|55442434|gb|CV734535.1|CV734535
EST:     GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGG                         GCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT
genomic: GGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGT

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: 61 (upstream exon), 57 (downstream exon)
Score: 31

GCGCTCCCGAATCAGCAGACGGTGGACTACCCCAGCTTCAAGCTCGTCATCGTCGGCGACGGCGGCACGGgttagcctcg ... tgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGTATGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaggctcgaaaatttctgtctgttctgaaaccaggcaatctttttgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGTATGAGC
                                          ttttgat  putative branch site (score: 31)
                                       tcttttt  CT-rich tract
                                     aatctttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatttataggattaaaaatttcttgtttcctgtgctcgaaattgccaggctcgaaaatttctgtctgttctgaaaccaggcaatctttttgatttgcagGCAAAACCACCTTTGTGAAGAGGCATTTGACTGGCGAGTTCGAGAAGAAGTATGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - -tttcttg
- - - - - - - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - - - - - -tgccagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaggca