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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacttagcttgctaatatagcagatatttagctatattctgcccaaagtttgctgaacagctatattttgcttatatagcattactattccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGCTCCTCTACCACTTGAACAATCTCCATCAG

Basic information

species Oryza sativa
transcript LOC_Os03g18370.1
intron # 2
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|117246185|gb|CT862605.1|CT862605
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
EST: gi|88433062|gb|CI569731.1|CI569731
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGAATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCAACAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
EST: gi|88385734|gb|CI566596.1|CI566596
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAAC-AAGGTGCACCAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
EST: gi|88311304|gb|CI570378.1|CI570378
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
EST: gi|88345043|gb|CI625889.1|CI625889
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
EST: gi|88341081|gb|CI638637.1|CI638637
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
EST: gi|88387528|gb|CI583046.1|CI583046
EST:     GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG                         GAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC
genomic: GGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGC

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: 71 (upstream exon), 61 (downstream exon)
Score: 12

GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAGgtgggtgctc ... ccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGCTCCTCTACCACTTGAACAATCTCCATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttgctgaacagctatattttgcttatatagcattactattccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGCTCCTCTACCACTTGAACAATCTCCATCAG
                                           ttccttattt  CT-rich tract
                 tatattttgcttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacttagcttgctaatatagcagatatttagctatattctgcccaaagtttgctgaacagctatattttgcttatatagcattactattccttatttagGAACGTTAGAAGACTTCTGCAGACTGGTGGAGTAAACCAAGGTGCACCAGCTCCTCTACCACTTGAACAATCTCCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - agcttgc
- - - - - - - - - - - - - - - - - - -ttctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa