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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaattagccctttccatatctgttgtgtttacttatgactatttcaattatatatattcaatcatgtttacccccatacatcaatttgataccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCTGACGGTGGGATATGCTGTTG

Basic information

species Oryza sativa
transcript LOC_Os11g24540.2
intron # 11
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|88243152|gb|CI244274.1|CI244274
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|88838737|gb|CI376275.1|CI376275
EST:     GATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAA-GGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|2310019|gb|C26174.1|C26174
EST:     GCTTTGGTGACATTATTTTCCCTGGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAN-AAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GCTTTGGTGACATTATTTTCCCTGG-ATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|38474789|gb|CF958922.1|CF958922
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|58691853|gb|CK080540.1|CK080540
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|58591329|gb|CF989637.1|CF989637
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|29664759|gb|CB661034.1|CB661034
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|25799734|gb|CA755695.1|CA755695
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|29667214|gb|CB663489.1|CB663489
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|29641729|gb|CB646736.1|CB646736
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|58696086|gb|CK084773.1|CK084773
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|58677052|gb|CK065739.1|CK065739
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|89173316|gb|CI041209.1|CI041209
EST:     TTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: TTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|88833460|gb|CI076941.1|CI076941
EST:     GGCTTTGGTGACATTATTTTGCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|88271842|gb|CI387895.1|CI387895
EST:     ACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGCCCTCTTCAATGGGTATTTTCTATGGCT
genomic: ACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|27578188|gb|CB000883.1|CB000883
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|29633639|gb|CB638648.1|CB638648
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|29677381|gb|CB673656.1|CB673656
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|86490199|gb|CI132832.1|CI132832
EST:     TTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: TTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|86426221|gb|CI071318.1|CI071318
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|86414835|gb|CI069238.1|CI069238
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|86483132|gb|CI125765.1|CI125765
EST:     TTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: TTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|218501626|gb|FG955998.1|FG955998
EST:     GCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGC-TCTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCAT-TCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|218504564|gb|FG954781.1|FG954781
EST:     GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: GGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
EST: gi|88245493|gb|CI245342.1|CI245342
EST:     CCTGGATTGCTAGTTGCATTCAGCTACAG                         ATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT
genomic: CCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCT

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: 71 (upstream exon), 71 (downstream exon)
Score: 107

TCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatact ... taccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCTGACGGTGGGATATGCTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattatatatattcaatcatgtttacccccatacatcaatttgataccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCTGACGGTGGGATATGCTGTTG
                                       atttgat  putative branch site (score: 107)
     atatatattcaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaattagccctttccatatctgttgtgtttacttatgactatttcaattatatatattcaatcatgtttacccccatacatcaatttgataccgtgtagATTTGATAGAGCAAGCAAAAGGGGCCTCTTCAATGGGTATTTTCTATGGCTGACGGTGGGATATGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - cttatga