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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaaccaaaaggaatagaatgctgttaatgcaacatttcacctctgcatccaacagttttaacaccatacaatttgtgctattttgtag

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 13
splice site 5'
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|58656234|gb|CK044914.1|CK044914
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTT
EST: gi|218490049|gb|FG963619.1|FG963619
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|33676232|gb|CF304471.1|CF304471
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|29642462|gb|CB647469.1|CB647469
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|218493259|gb|FG949070.1|FG949070
EST:     CTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: CTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|33676868|gb|CF305107.1|CF305107
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58673473|gb|CK062159.1|CK062159
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58670000|gb|CK058686.1|CK058686
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58672496|gb|CK061182.1|CK061182
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58681408|gb|CK070095.1|CK070095
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58585822|gb|CF984130.1|CF984130
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|29626361|gb|CB631372.1|CB631372
EST:     CAATTGAGGAGTGCCGCCAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: CAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58607251|gb|CK035284.1|CK035284
EST:     AGGCTCCAATGGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|218502862|gb|FG946696.1|FG946696
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|218499296|gb|FG965743.1|FG965743
EST:     AGGCTCCAATTGAGGAGTGCCGCAACAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58665642|gb|CK054328.1|CK054328
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCC
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCC
EST: gi|33676662|gb|CF304901.1|CF304901
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCANGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|8956808|gb|BE230611.1|BE230611
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCT
EST: gi|58597534|gb|CK008062.1|CK008062
EST:     AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAG                         GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTT
genomic: AGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTT

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: 75 (upstream exon), 61 (downstream exon)
Score: 40

ACAAAGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaacc ... tattttgtagGGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAAGGCTCCAATTGAGGAGTGCCGCAAGAAGGTTTGGCTGCTGGATTCAAAGgtatagaaccaaaaggaatagaatgctgttaatgcaacatttcacctctgcatccaacagttttaacaccatacaatttgtgctattttgtag

- - - - - - -  GAGGAG
- - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - -  GCTGGA