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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagagttaactaagacggttctataatattctattgcatataaatattctgaccttatttgttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG

Basic information

species Oryza sativa
transcript LOC_Os01g33000.1
intron # 3
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|218493642|gb|FG944469.1|FG944469
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|87006610|gb|CI294993.1|CI294993
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|33680042|gb|CF308281.1|CF308281
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|29681976|gb|CB678251.1|CB678251
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|33685867|gb|CF314106.1|CF314106
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|218487332|gb|FG968263.1|FG968263
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|218493643|gb|FG944470.1|FG944470
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|33810073|gb|CF330924.1|CF330924
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCATGACTGAGGACCCTTAAAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|218498668|gb|FG952677.1|FG952677
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|33680411|gb|CF308650.1|CF308650
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
EST: gi|218480683|gb|FG945057.1|FG945057
EST:     AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAG                         ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT
genomic: AATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGT

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: 62 (upstream exon), 48 (downstream exon)
Score: 28

CTCAAGTGATGATGGTGAATCAGGAGATTTGCATGGCCGCTTGCTCTTTCAATACCTTGAGTTTGATTCTCCATTTTGTCGTGAACCATTGACTGATAAGgcaagagtta ... gttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttctataatattctattgcatataaatattctgaccttatttgttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG
                               ttctgac  putative branch site (score: 28)
                                     ccttatttgttctttc  CT-rich tract
      tataatattctattgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagagttaactaagacggttctataatattctattgcatataaatattctgaccttatttgttctttcagATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG