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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaagtcactatctaccttttgtgattgtagttagtgccatatttcttatccttcttaattggatgaaaacagtagaatgatatctggatgaac...

Basic information

species Oryza sativa
transcript LOC_Os01g07910.1
intron # 12
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|88267058|gb|CI378993.1|CI378993
EST:     TGATGAATCAAATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86866447|gb|CI343418.1|CI343418
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86598869|gb|CI355486.1|CI355486
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88238022|gb|CI237871.1|CI237871
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86420283|gb|CI056272.1|CI056272
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|163927043|gb|EG715166.1|EG715166
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCACAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86824941|gb|CI358146.1|CI358146
EST:     TGATGAATCATATATCCGCTGAC-AGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88507988|gb|CI435494.1|CI435494
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88376370|gb|CI535474.1|CI535474
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|163928246|gb|EG714638.1|EG714638
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAA
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAA
EST: gi|89184292|gb|CI046857.1|CI046857
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88485015|gb|CI422286.1|CI422286
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88463003|gb|CI522114.1|CI522114
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|27554208|gb|CA998108.1|CA998108
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88319567|gb|CI518411.1|CI518411
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86546020|gb|CI186226.1|CI186226
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86250752|gb|CI007615.1|CI007615
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|86494415|gb|CI137048.1|CI137048
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
EST: gi|88485354|gb|CI422625.1|CI422625
EST:     TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG                         CTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG
genomic: TGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAG

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: 43 (upstream exon), 27 (downstream exon)
Score: 2

GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaa ... tactctgcagCTCACCGGCATTCTGAAAGAGTTAGGATACACTGCAGAGATGGTATACAAGTTCTGAGTGCGTCTTCAAGACGTTAGAATGCTGACATGCTTGCTGCAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAGgtaatgtgaagtcactatctaccttttgtgattgtagttagtgccatatttcttatccttcttaattggatgaaaacagtagaatgatatctggatgaac

- - - - - - - - - - - - - - - - - - - - - -  GCAAAG