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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacgaattaaaattaaaattccccaaaaaaatatttatttgacaagaaataatatatgtgctcgatctaattgacgaaccttgtaataaaaataaacaatccaactattag

Basic information

species Oryza sativa
transcript LOC_Os02g01220.1
intron # 4
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|86887184|gb|CI325999.1|CI325999
EST:     TTGTGGAACAGTTCTCGTCGCTAGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|58593836|gb|CF992144.1|CF992144
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|33666398|gb|CF297365.1|CF297365
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88289261|gb|CI553237.1|CI553237
EST:     TGGAGCAGTTCTCGTCGCTGGTGAGCCAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88456290|gb|CI560893.1|CI560893
EST:     CGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTNTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: CGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|86525933|gb|CI166139.1|CI166139
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88409341|gb|CI559439.1|CI559439
EST:     TGGACCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|86547077|gb|CI187283.1|CI187283
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|86545060|gb|CI185266.1|CI185266
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88202886|gb|CI200738.1|CI200738
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88998270|gb|CI038155.1|CI038155
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88977408|gb|CI025145.1|CI025145
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88517358|gb|CI445012.1|CI445012
EST:     AAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: AAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88239644|gb|CI238806.1|CI238806
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88201999|gb|CI202354.1|CI202354
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88201185|gb|CI201540.1|CI201540
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCC-AAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88200758|gb|CI200608.1|CI200608
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|87034626|gb|CI189250.1|CI189250
EST:     TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: TTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
EST: gi|88322931|gb|CI548025.1|CI548025
EST:     AAGAGGAGCATGTGGTTGTG                         GGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA
genomic: AAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAA

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: 71 (upstream exon), 54 (downstream exon)
Score: 55

GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacg ... caactattagGGGTGCCAAAGCGGGAAGAGGTCGGAGCTAGCATGCGTTGATCTCCTTGAAGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTGgtacgatacgaattaaaattaaaattccccaaaaaaatatttatttgacaagaaataatatatgtgctcgatctaattgacgaaccttgtaataaaaataaacaatccaactattag

- - - - - - - - - - - GTGGAG
- - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA