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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaaaaaaaagtgagaaaagatttttttttttgaaatttttaataaaggttacatacattagcagtttgatgttggtggccttcaacattgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGATGGGATCACTCCTTCACCGAGTACATTAAATACGAGATTGGATGGGAGT

Basic information

species Oryza sativa
transcript LOC_Os11g29490.3
intron # 2
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|88364123|gb|CI610467.1|CI610467
EST:     GCCGCCCCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88301456|gb|CI597149.1|CI597149
EST:     CCGCCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAC                         -TGGGTGGAAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: CCGCC-TCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88364693|gb|CI612508.1|CI612508
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGG
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGT-GGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGG
EST: gi|88694254|gb|CI738292.1|CI738292
EST:     GCCCCCTCCNGCTGTACGGCCCTACCCTCGTGGTCGCCCATCACCCCCAG                         CTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88397921|gb|CI583239.1|CI583239
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCCATCGTCCTGCTCTGGGG
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGC-ATCGTCCTGCTCTGGGG
EST: gi|88393212|gb|CI616696.1|CI616696
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88362606|gb|CI608755.1|CI608755
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88300206|gb|CI582440.1|CI582440
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88362123|gb|CI607123.1|CI607123
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88575694|gb|CI669839.1|CI669839
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCCTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88726828|gb|CI750483.1|CI750483
EST:     CCGCCTCAAGCCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAC                         GTGGGTGGCAAGCTTCTCGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: CCGCCTCAAGC-TGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
EST: gi|88395315|gb|CI611232.1|CI611232
EST:     GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAG                         GTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA
genomic: GCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGA

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: 43 (upstream exon), 73 (downstream exon)
Score: 2

CCGTCTCGGCACCGACGAGGCGACTGGGCTGACGGAGGAGGAGGCGGCGCGCCGCCTCAAGCTGTACGGGCCTAACCTCGTGGTCGCCCATCACCCCCAGgttcgctttg ... tgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGATGGGATCACTCCTTCACCGAGTACATTAAATACGAGATTGGATGGGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggttacatacattagcagtttgatgttggtggccttcaacattgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGATGGGATCACTCCTTCACCGAGTACATTAAATACGAGATTGGATGGGAGT
                    gtttgat  putative branch site (score: 2)
         atacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagaaaaaaaagtgagaaaagatttttttttttgaaatttttaataaaggttacatacattagcagtttgatgttggtggccttcaacattgtgcttcagGTGGGTGGCAAGCTTCTTGCTACACTAAAGTGCATCGTCCTGCTCTGGGGATGGGATCACTCCTTCACCGAGTACATTAAATACGAGATTGGATGGGAGT

- -aaaaaaa
- - - - - - - agaaaaga
- - - - - - - - - - - - - - - - - - - - - aataaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - -catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggtg