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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcccaactaatttgttaatattacttaatattctatacttcttttgggatgaagtcaatactctacttggttcgctgacgtttgttgttattgttcaatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGACCATGAAGCAACAGAT

Basic information

species Oryza sativa
transcript LOC_Os10g37210.1
intron # 13
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|218502645|gb|FG955089.1|FG955089
EST:     GCATTTGAATCTGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29615151|gb|CB620164.1|CB620164
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29657656|gb|CB653931.1|CB653931
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29675569|gb|CB671844.1|CB671844
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29662394|gb|CB658669.1|CB658669
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTTTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|218486085|gb|FG956984.1|FG956984
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29637767|gb|CB642776.1|CB642776
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|86859459|gb|CI278866.1|CI278866
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCANGGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29669361|gb|CB665636.1|CB665636
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29667105|gb|CB663380.1|CB663380
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29676401|gb|CB672676.1|CB672676
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29659147|gb|CB655422.1|CB655422
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29681493|gb|CB677768.1|CB677768
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA

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: 50 (upstream exon), 67 (downstream exon)
Score: 21

GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGACCATGAAGCAACAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtcaatactctacttggttcgctgacgtttgttgttattgttcaatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGACCATGAAGCAACAGAT
                      cgctgac  putative branch site (score: 21)
                                                ttttt  putative PPT
                                     ttattgttcaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcccaactaatttgttaatattacttaatattctatacttcttttgggatgaagtcaatactctacttggttcgctgacgtttgttgttattgttcaatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGACCATGAAGCAACAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA