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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtctatagttatctttcagtagttgtttgtgcagttttggtattcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC

Basic information

species Oryza sativa
transcript LOC_Os01g59930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 1
--cattgtcta-----tagttatctttcagtagttgtttgtgcagttttggtattcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC
   ||   | |     || || |  || |||  ||| || |||| ||   |  || ||||    |  ||  |||  || ||| ||     | || ||    | | |||||| ||||||||||||||||||| |||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| || |||||||||||||||||
tttatcacccaaaaaatatttgtgcttaagt--ttgcttctgcaattcaag-gttaatgcgttatagctcaatt--tgattgttgt--gctgttgttttggcattagGCTGCTTGGATCCTGAGAACTTCAGGAAGTTCAAACTTGTTGAAAAGAAGCAAATAAGTCATAATGTTGCCAGGTTCAAGTTCGCTCTTCCAACTCCAAC
















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|88362855|gb|CI614211.1|CI614211
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88763102|gb|CI772658.1|CI772658
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|117244284|gb|CT843075.1|CT843075
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|58685456|gb|CK074143.1|CK074143
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|58684839|gb|CK073526.1|CK073526
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88736272|gb|CI759780.1|CI759780
EST:     GTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCCAAGG                         -CTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAG
genomic: GTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCC-AAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAG
EST: gi|58595179|gb|CF993487.1|CF993487
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88388215|gb|CI627754.1|CI627754
EST:     GGTCGCCGCGGGCGGGGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|2309816|gb|C25971.1|C25971
EST:     GGTCGCCGCGNGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGNTCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|25801449|gb|CA757410.1|CA757410
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|58603188|gb|CK013716.1|CK013716
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|427743|gb|D23879.1|D23879
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88391603|gb|CI600792.1|CI600792
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC

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: 74 (upstream exon), 70 (downstream exon)
Score: 94

CACGGGGAGAGCGTCCAGACCACGGTGGCCATCGCCGTCGCCGTCGTCGCGGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC
                  tattgat  putative branch site (score: 94)
                               tgccatttatttttcc  putative PPT
                                   atttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgtctatagttatctttcagtagttgtttgtgcagttttggtattcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC

- - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgcc