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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacgaatcccccctcttctcctctcccatttgctgcttcgctctcgcgatttagttgctgaccgccatgtgcgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTCGCCTCCGTCGCCACCTTCGGGTTCCGCGGGGAGGCGCTCAGCTCGCTCT

Basic information

species Oryza sativa
transcript LOC_Os02g37920.1
intron # 1
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|88371534|gb|CI602712.1|CI602712
EST:     CCTTCACCGTCGCCGACAAGGGGACCGGCATCTCCCCCAACAATTTCCAG                         GCGCTCGCTCTGAAGCAACACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88327455|gb|CI645243.1|CI645243
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGNGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88461666|gb|CI695508.1|CI695508
EST:     CTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCCAC-AATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCC-ACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88428473|gb|CI564941.1|CI564941
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCATACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88359296|gb|CI679820.1|CI679820
EST:     CCTTCANCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|95101715|gb|CI697154.1|CI697154
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88664726|gb|CI702008.1|CI702008
EST:     CCTTCACCGTCGCCGACAANGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88412354|gb|CI688697.1|CI688697
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88664477|gb|CI697865.1|CI697865
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88392476|gb|CI611742.1|CI611742
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88313355|gb|CI671464.1|CI671464
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88400909|gb|CI616914.1|CI616914
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTC
EST: gi|88718473|gb|CI741983.1|CI741983
EST:     CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAG                         GCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCG
genomic: CCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCG

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: 69 (upstream exon), 69 (downstream exon)
Score: 7

CGCCGGCGCCACCACCGTCGAGGTCACCCTCCGCTCCTACGGCGAGGACTCCTTCACCGTCGCCGACAACGGCACCGGCATCTCCCCCACCAATTTCCAGgcacgaatcc ... cgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTCGCCTCCGTCGCCACCTTCGGGTTCCGCGGGGAGGCGCTCAGCTCGCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgctgcttcgctctcgcgatttagttgctgaccgccatgtgcgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTCGCCTCCGTCGCCACCTTCGGGTTCCGCGGGGAGGCGCTCAGCTCGCTCT
                             tgctgac  putative branch site (score: 7)
                                             cgcttctc  putative PPT
                      atttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacgaatcccccctcttctcctctcccatttgctgcttcgctctcgcgatttagttgctgaccgccatgtgcgcttctcagGCGCTCGCTCTGAAGCACCACACCTCCAAGATCTCGGACTTCGGCGACCTCGCCTCCGTCGCCACCTTCGGGTTCCGCGGGGAGGCGCTCAGCTCGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC