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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccaccgtctccccccgcgccgagaatctcggagatctcgtgaaaaaagataaaaaagatcgtgtctttttcttcgctgcttcttggatcgagatcccaatcctttgtggtctgttttttcgcttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG

Basic information

species Oryza sativa
transcript LOC_Os04g47580.1
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|88401846|gb|CI591173.1|CI591173
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGC-AAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
EST: gi|88722849|gb|CI746359.1|CI746359
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCA
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCA
EST: gi|58661771|gb|CK050451.1|CK050451
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGGTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
EST: gi|58658155|gb|CK046835.1|CK046835
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
EST: gi|88721535|gb|CI744834.1|CI744834
EST:     GTNGGGGCGCCGCCGCACCCGTCCGNGATCGCCAAGAAGCCGATGCTAGA                         CAAGAGTGGGAAGGAAGAGCAGAAGCGTGCA
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCA
EST: gi|86831971|gb|CI305197.1|CI305197
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
EST: gi|88406938|gb|CI578466.1|CI578466
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCTATCGCCAATAAGCCGATGCTAGA                         TAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
EST: gi|58672181|gb|CK060867.1|CK060867
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
EST: gi|88695221|gb|CI739259.1|CI739259
EST:     CTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAG
genomic: -TCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAG
EST: gi|88694046|gb|CI738084.1|CI738084
EST:     GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGA                         GAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC
genomic: GTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCC

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: 66 (upstream exon), 55 (downstream exon)
Score: 3

AGATGGGGAACCGGAGGCCGCTCAGGGACATCAACAACCTCGTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccacc ... cttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcttggatcgagatcccaatcctttgtggtctgttttttcgcttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG
                                 tctgttttttcgcttt  CT-rich tract
                                   tgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccaccgtctccccccgcgccgagaatctcggagatctcgtgaaaaaagataaaaaagatcgtgtctttttcttcgctgcttcttggatcgagatcccaatcctttgtggtctgttttttcgcttttgtcagGAAGAGTGGGAAGGAAGAGCAGAAGCCTGCATTGGTGGTGAGCCACCGGCCTATGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG