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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaagctgattaattaccaatttagctgacagcaacttgaggtgtgcttctgttaaatggattaacgaagaatctcatcgttttttttccctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA

Basic information

species Oryza sativa
transcript LOC_Os01g41220.1
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|88518848|gb|CI445694.1|CI445694
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|38472703|gb|CF956835.1|CF956835
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88977533|gb|CI025269.1|CI025269
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88508981|gb|CI436487.1|CI436487
EST:     GTTCAACGCCAGCCTCGAGTGCCCCNCCAAAGCGGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: -TTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88241693|gb|CI241542.1|CI241542
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86522577|gb|CI162783.1|CI162783
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87028437|gb|CI263779.1|CI263779
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88236964|gb|CI236813.1|CI236813
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86592601|gb|CI253282.1|CI253282
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                    
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAGgtaaaggtac ... ccttt
EST: gi|18387710|gb|BM420908.1|BM420908
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCCAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88204552|gb|CI204401.1|CI204401
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86597557|gb|CI282681.1|CI282681
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86509682|gb|CI152315.1|CI152315
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTCGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|29680632|gb|CB676907.1|CB676907
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88240099|gb|CI239261.1|CI239261
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86506792|gb|CI149425.1|CI149425
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTAAAGGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGT------CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGG
EST: gi|88203908|gb|CI203757.1|CI203757
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                    
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAGgtaaaggtac ... ccttt
EST: gi|87028385|gb|CI263727.1|CI263727
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86507626|gb|CI150259.1|CI150259
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88384832|gb|CI559100.1|CI559100
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|29680631|gb|CB676906.1|CB676906
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88210746|gb|CI210595.1|CI210595
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87013474|gb|CI267175.1|CI267175
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTAAAGGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGT------CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGG
EST: gi|88998026|gb|CI037911.1|CI037911
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86545808|gb|CI186014.1|CI186014
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87018749|gb|CI254457.1|CI254457
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88205075|gb|CI204924.1|CI204924
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                    
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAGgtaaaggtac ... ccttt
EST: gi|87031417|gb|CI261791.1|CI261791
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|117247693|gb|CT848586.1|CT848586
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86823314|gb|CI256319.1|CI256319
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88204837|gb|CI202688.1|CI202688
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87025174|gb|CI265739.1|CI265739
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTAAAGGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGT------CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGG
EST: gi|88243737|gb|CI242859.1|CI242859
EST:     CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG

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: 49 (upstream exon), 75 (downstream exon)
Score: 40

GAGCTCGTCTTCGAGGTCGGCTCCGTCTCCGCCAAGTTCCCCGCCCGCCACTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGgtaaaggtac ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttctgttaaatggattaacgaagaatctcatcgttttttttccctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA
               gattaac  putative branch site (score: 40)
                            tctcatcgtttttttt  putative PPT
                                    tttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaagctgattaattaccaatttagctgacagcaacttgaggtgtgcttctgttaaatggattaacgaagaatctcatcgttttttttccctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA

- - -gctgatt
- - - - - - - - - - - - -gctgaca
- - - - - - - - - - - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acgaagaa