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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactttatattgtttctaatctcatcctgaaagctcgactgcatagcttttcaagatattgctactgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATATAAATAGCAACACTGCACACATGGAATTATGCGGCTCTATCTAGATTTG

Basic information

species Oryza sativa
transcript LOC_Os02g25580.1
intron # 20
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|86889063|gb|CI314679.1|CI314679
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|84117192|gb|CD150959.1|CD150959
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|86502532|gb|CI145165.1|CI145165
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|89195197|gb|CI051310.1|CI051310
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88439440|gb|CI536412.1|CI536412
EST:     GTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: GTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|86861363|gb|CI328113.1|CI328113
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|218505032|gb|FG952958.1|FG952958
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTTAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|18386204|gb|BM419403.1|BM419403
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|86873511|gb|CI329889.1|CI329889
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88483914|gb|CI421185.1|CI421185
EST:     TGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: TGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|86602824|gb|CI357188.1|CI357188
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|86870282|gb|CI319388.1|CI319388
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|89173015|gb|CI040908.1|CI040908
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88265340|gb|CI369114.1|CI369114
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|86845413|gb|CI340467.1|CI340467
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCACTTCATCACC                         AAACTGAAGATGATGTCACTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|163922673|gb|EG714174.1|EG714174
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|29626796|gb|CB631807.1|CB631807
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|89174016|gb|CI041909.1|CI041909
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88515926|gb|CI443580.1|CI443580
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|29626758|gb|CB631769.1|CB631769
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88384265|gb|CI551191.1|CI551191
EST:     AAGTCATACTTGGTTTATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|4715056|gb|AU056173.1|AU056173
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88261074|gb|CI364650.1|CI364650
EST:     GTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: GTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|29689435|gb|CB685710.1|CB685710
EST:     AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG                         AAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
EST: gi|88262689|gb|CI366463.1|CI366463
EST:     AAGTCATACTTGGTTCATCTAGTGTGGATGATCCTCCCCAGTTCATCACG                         AAAC-GAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA
genomic: AAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATA

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: 56 (upstream exon), 62 (downstream exon)
Score: 22

TTACGTGCTGTGCACAAGCTTACATCCAAGCTAAAGCGGGAAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactt ... ctgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATATAAATAGCAACACTGCACACATGGAATTATGCGGCTCTATCTAGATTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcatcctgaaagctcgactgcatagcttttcaagatattgctactgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATATAAATAGCAACACTGCACACATGGAATTATGCGGCTCTATCTAGATTTG
                                 aagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactttatattgtttctaatctcatcctgaaagctcgactgcatagcttttcaagatattgctactgcctgcagAAACTGAAGATGATGTCAGTCGATGAACTGACGCTGGATGATCTTCAAATATAAATAGCAACACTGCACACATGGAATTATGCGGCTCTATCTAGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA