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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcagccttttttttagctctgttaatatcatgattaaatttatgaagtcttgcataactctaccccgtgtctcatgatatttttttttctggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGACTCGATTCAACAAGGACAGGAATACAGTCGACTACAACTATATTGCAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g73120.1
intron # 6
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|22306364|gb|BQ907586.1|BQ907586
EST:     CCTGTGTTCTTGGCACTCGTGCTGGCCCAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|29668922|gb|CB665197.1|CB665197
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|218501560|gb|FG959366.1|FG959366
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGATCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|29661521|gb|CB657796.1|CB657796
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|33654477|gb|CF277091.1|CF277091
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|427638|gb|D23771.1|D23771
EST:     CCTGTNTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTNAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|86853925|gb|CI329371.1|CI329371
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTCCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|3767617|gb|AU031644.1|AU031644
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCCAGCGGTGGAAGGTCCAAGTTGGTTGCAGTGAGAGAG
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATT-CCAGCGGTGGAAGGT-CAAGTTGGTTGCAGTGAGAGAG
EST: gi|88507528|gb|CI435034.1|CI435034
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|88521398|gb|CI449081.1|CI449081
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|157651623|gb|EX451257.1|EX451257
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|88268843|gb|CI377747.1|CI377747
EST:     CCTGTGTTCTTGGCACTCATGCT-GCCAAAAGGACTGTTGAACCAGAAA-                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|27578313|gb|CB001008.1|CB001008
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|86853877|gb|CI329323.1|CI329323
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAACGGTGGAAGGTCAAATTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|86835917|gb|CI346097.1|CI346097
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|88959711|gb|CI002321.1|CI002321
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|33823206|gb|CF337403.1|CF337403
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
EST: gi|29671029|gb|CB667304.1|CB667304
EST:     CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAG                         GGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC
genomic: CCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGAC

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), 72 (downstream exon)
Score: 9

ATCAAATTGTTAGCGGTCATACTCTTAAGCATCTAGCTGCTGCAATGGTGCCTGTGTTCTTGGCACTCATGCTGGCCAAAAGGACTGTTGAACCAGAAAGgtatgcttta ... tggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGACTCGATTCAACAAGGACAGGAATACAGTCGACTACAACTATATTGCAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtcttgcataactctaccccgtgtctcatgatatttttttttctggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGACTCGATTCAACAAGGACAGGAATACAGTCGACTACAACTATATTGCAGTT
       gcataac  putative branch site (score: 9)
 tatttttttttct  putative PPT
 tcatgatatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagccttttttttagctctgttaatatcatgattaaatttatgaagtcttgcataactctaccccgtgtctcatgatatttttttttctggaatgcagGGTAAGTTTATTCCAGCGGTGGAAGGTCAAGTTGGTTGCAGTGAGAGAGACTCGATTCAACAAGGACAGGAATACAGTCGACTACAACTATATTGCAGTT

- - - - - - - - - tctgtta
- - - - - - - - - - - - - - tcatgat
- - - - - - - - - - - - - - - - - - - - - - - - tcttgca