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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttaatcggactttcttcttaatattcttatgactaacatttcaatagcaacatttgcttttcctgaaaatatgcttgtcttatttccttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAGAGCTGTGCCGTTCTATAGAGTGGTTCCTCTCCCGGAGGGCCACCGGCAG

Basic information

species Oryza sativa
transcript LOC_Os12g19350.1
intron # 8
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|58664363|gb|CK053049.1|CK053049
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88519487|gb|CI447141.1|CI447141
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|29685642|gb|CB681917.1|CB681917
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|58695843|gb|CK084530.1|CK084530
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88511815|gb|CI439321.1|CI439321
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88902143|gb|CI374751.1|CI374751
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88517931|gb|CI444820.1|CI444820
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|218496318|gb|FG954188.1|FG954188
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|3767294|gb|AU031404.1|AU031404
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88473931|gb|CI411202.1|CI411202
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|15847274|gb|BI795550.1|BI795550
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACCAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|218491607|gb|FG958897.1|FG958897
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|86428812|gb|CI075493.1|CI075493
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TNATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAA
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAA-
EST: gi|88284496|gb|CI405942.1|CI405942
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88483496|gb|CI420767.1|CI420767
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|88974062|gb|CI002724.1|CI002724
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACC-CAAAA
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAA-
EST: gi|29685641|gb|CB681916.1|CB681916
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTNGTT-GATGATGA
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTT-GTTTGATGATGA
EST: gi|88839574|gb|CI005362.1|CI005362
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
EST: gi|109711804|gb|CI028974.1|CI028974
EST:     CTAATCGTAAGAGGAAATCTGACGA                         TTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG
genomic: CTAATCGTAAGAGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAG

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: 66 (upstream exon), 66 (downstream exon)
Score: 45

AGGAAATCTGACGAgtaagtattt ... cttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAGAGCTGTGCCGTTCTATAGAGTGGTTCCTCTCCCGGAGGGCCACCGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatagcaacatttgcttttcctgaaaatatgcttgtcttatttccttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAGAGCTGTGCCGTTCTATAGAGTGGTTCCTCTCCCGGAGGGCCACCGGCAG
                                cttgtcttatttcctt  CT-rich tract
                      tgaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttttaatcggactttcttcttaatattcttatgactaacatttcaatagcaacatttgcttttcctgaaaatatgcttgtcttatttccttttggcagTTATCTACTCTTGTTTGATGATGACGAGGAGGATGGAAATCTACCACAAAGAGCTGTGCCGTTCTATAGAGTGGTTCCTCTCCCGGAGGGCCACCGGCAG

- - - - - - - - - - - - - - tcttatg
- - - - - - - - - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcttg