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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTGTAGATGACTTGAGAGCTGATGGCATTGAAACGGGCGGCAGATATTATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattggtgtgtttacagtatgataggagaaacatgctgccatcgcagacatggatctattcaatccttacatatgtttgtttcatcatttgcatt...

Basic information

species Oryza sativa
transcript LOC_Os02g57400.1
intron # 3
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|218488536|gb|FG960950.1|FG960950
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTC-AAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGACTGCTGATGA
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGA-TGCTGATGA
EST: gi|218482213|gb|FG969064.1|FG969064
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|29623882|gb|CB628893.1|CB628893
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|29642503|gb|CB647510.1|CB647510
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|86477326|gb|CI119959.1|CI119959
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|5055992|gb|AU075371.1|AU075371
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|218496542|gb|FG959296.1|FG959296
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTAGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|29642372|gb|CB647379.1|CB647379
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
EST: gi|218485764|gb|FG955746.1|FG955746
EST:     ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAG                         CTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT
genomic: ATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGAT

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: 64 (upstream exon), 46 (downstream exon)
Score: 17

AAGTGTAGATGACTTGAGAGCTGATGGCATTGAAACGGGCGGCAGATATTATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattg ... gacttttcagCTTATGGAGGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTGTAGATGACTTGAGAGCTGATGGCATTGAAACGGGCGGCAGATATTATTCCTCATGCTGCAGTTCACCAAAGGTGTCAGATTGCCCTTCAAAAGAGgtatgcattggtgtgtttacagtatgataggagaaacatgctgccatcgcagacatggatctattcaatccttacatatgtttgtttcatcatttgcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG