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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttcatactctttctttaatttgcaaaaaatatgtttgtgaattctcactctggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCTATGCGGCTGAAGGCATCCCCCTCAGGTCTGCTGCTGAAGGCCTCCCTCT

Basic information

species Oryza sativa
transcript LOC_Os01g65986.1
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|86250772|gb|CI007635.1|CI007635
EST:     ACGAAAGATATGGTCGATG                         GACTCCCACCGACTCTACCTATCCGAATACCGAGACATGATGAAGATGGCT
genomic: ACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|88520773|gb|CI446429.1|CI446429
EST:     TATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: TATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86537742|gb|CI177948.1|CI177948
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86537849|gb|CI178055.1|CI178055
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86425672|gb|CI070769.1|CI070769
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86486801|gb|CI129434.1|CI129434
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86493006|gb|CI135639.1|CI135639
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86603251|gb|CI112011.1|CI112011
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|86425888|gb|CI070985.1|CI070985
EST:     AGATATGGTCGATG                         GACTCCCACCAACTTTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: AGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|58604427|gb|CK014955.1|CK014955
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
EST: gi|88833476|gb|CI076957.1|CI076957
EST:     CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATG                         GACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT
genomic: CATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCT

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: 65 (upstream exon), 74 (downstream exon)
Score: 23

GATCGTCAAAATCCAACTCAAATTGTGACAGAGATGTGTGGTTTTGTTACCATCCTTTCTGGGACGTTTCTTCTTCACAAGACGAAAGATATGGTCGATGgtatgatttc ... ggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCTATGCGGCTGAAGGCATCCCCCTCAGGTCTGCTGCTGAAGGCCTCCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttctttaatttgcaaaaaatatgtttgtgaattctcactctggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCTATGCGGCTGAAGGCATCCCCCTCAGGTCTGCTGCTGAAGGCCTCCCTCT
                                   ttctcac  putative branch site (score: 23)
       tttaatttgcaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatttcatactctttctttaatttgcaaaaaatatgtttgtgaattctcactctggcctcgtagGACTCCCACCAACTCTACCTATCCGAATACCGAAACATGATGAAGATGGCTATGCGGCTGAAGGCATCCCCCTCAGGTCTGCTGCTGAAGGCCTCCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG