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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctcgagccgcctccctctccttctttatcctctttttttcaaggcctgagtctcacggctggaatcctcgccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAGCGCTGCAAGGACCAAATCGACTGGAAGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g55730.1
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|88302743|gb|CI668589.1|CI668589
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|88739397|gb|CI762905.1|CI762905
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|33381195|gb|CF196538.1|CF196538
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|38470771|gb|CF954902.1|CF954902
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|428826|gb|D24982.1|D24982
EST:     AGAACCGCTACG-GTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|88718954|gb|CI742464.1|CI742464
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|88727187|gb|CI750842.1|CI750842
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|88420754|gb|CI564590.1|CI564590
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|88296284|gb|CI667674.1|CI667674
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
EST: gi|66932185|gb|CX119033.1|CX119033
EST:     AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACC                         GAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG
genomic: AGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAG

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: 67 (upstream exon), 48 (downstream exon)
Score: 23

TCGCGGGGGGAGGAGAGCGATGTCGAAGCGGCAGGGTCCCCCGAAGCATCAGAACCGCTACGCGTGGAAGCCCAACCTCGGGCAGAAGATCAACGAGACCgtgagtcctc ... gccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAGCGCTGCAAGGACCAAATCGACTGGAAGAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcctctttttttcaaggcctgagtctcacggctggaatcctcgccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAGCGCTGCAAGGACCAAATCGACTGGAAGAGAAG
                         gtctcac  putative branch site (score: 23)
                                        tcctcgcc  putative PPT
        tttttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcctcgagccgcctccctctccttctttatcctctttttttcaaggcctgagtctcacggctggaatcctcgccgctgcagGAGCCCGGCGGCAGGTTCCGTCCTTTGTCGGAGATCACCGGCGTCTGCCAGCGCTGCAAGGACCAAATCGACTGGAAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA