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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgttctttgtctctctgccctcctccatttttgacttatagttcaggactgtatttgcttgcttttttgcgccaacagccagatggttatagatttaattgagatgcgtggtgctcaaacatggcttcctttttacattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAGCCATGTCATCCTGGCCACAGGCATATGTGGTTGACGG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.1
intron # 16
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|29628841|gb|CB633852.1|CB633852
EST:     GAAATTTTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTCGTTGCGTCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|24468848|gb|CA305797.1|CA305797
EST:     ATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCGTCAGACCGGCCAATGGGCGATGTTCCAG
genomic: ATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29638287|gb|CB643296.1|CB643296
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29613155|gb|CB618168.1|CB618168
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTTGTTGCGTCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29613395|gb|CB618408.1|CB618408
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCGTCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29644979|gb|CB649986.1|CB649986
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29613120|gb|CB618133.1|CB618133
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTCGTTGCGTCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|33801021|gb|CF326384.1|CF326384
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29633044|gb|CB638053.1|CB638053
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|86863868|gb|CI332862.1|CI332862
EST:     CAGGATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: CAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTCGTTGCA
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCA
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|86896081|gb|CI330061.1|CI330061
EST:     TTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: TTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|89167683|gb|CI018289.1|CI018289
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTCGTTGCGTCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|8856640|gb|AU093958.1|AU093958
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|15858543|gb|BI811355.1|BI811355
EST:     TCCTCCTGTGCAGT---                         CA-GGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: TCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|58589430|gb|CF987738.1|CF987738
EST:     GTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCGATGGGCGATGTTCCAG
genomic: GTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|88835185|gb|CI370488.1|CI370488
EST:     GCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|86435343|gb|CI106576.1|CI106576
EST:     AAATCCTCCTGTGCAGTC-G                         --GGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: AAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29663527|gb|CB659802.1|CB659802
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGT---                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|29656192|gb|CB652467.1|CB652467
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         CAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|86886525|gb|CI322757.1|CI322757
EST:     GTACCCA-GATTT-AAAATCCTCCTCTCCAGT---                         CAGGNTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
genomic: GTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAG
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAG                         --GG-TTTTGGCCTCTCGTTGCATCANNNNGGCCAATGGGCGATGTTCCA
genomic: GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCA

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: 46 (upstream exon), 46 (downstream exon)
Score: 5

GAAATTCTGCTGTACCCAGGATTTGAAAATCCTCCTGTGCAGTCAGgtccgttctt ... cattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAGCCATGTCATCCTGGCCACAGGCATATGTGGTTGACGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttaattgagatgcgtggtgctcaaacatggcttcctttttacattatttagCAGGGTTTTGGCCTCTCGTTGCATCAGACCGGCCAATGGGCGATGTTCCAGCCATGTCATCCTGGCCACAGGCATATGTGGTTGACGG
  atttaat  putative branch site (score: 5)
                                  cttcctttttacatt  putative PPT
                                       tttttacattattta  TA-rich tract