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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcttcttatttgacatattggatatttataaggaccatgcccatatatattttcctcatggctgtattttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 9
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|27577068|gb|CA999762.1|CA999762
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|89191950|gb|CI250891.1|CI250891
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|89166280|gb|CI103370.1|CI103370
EST:     TTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|5701695|gb|AU063482.2|AU063482
EST:     GCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: GCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|86893269|gb|CI313403.1|CI313403
EST:     TGTGGATTT-GCACCAGGAGAGCTTCTGGAGGTGGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|86593940|gb|CI260169.1|CI260169
EST:     GTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: GTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACT-CCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|38475250|gb|CF959383.1|CF959383
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|9864980|gb|AU100730.1|AU100730
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|58690219|gb|CK078906.1|CK078906
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAA
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAA
EST: gi|87021256|gb|CI295315.1|CI295315
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|58597827|gb|CK008355.1|CK008355
EST:     ACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: ACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
EST: gi|163920798|gb|EG710061.1|EG710061
EST:     TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAG                         TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT
genomic: TGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTT

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: 73 (upstream exon), 71 (downstream exon)
Score: 17

AGCCCAAATTTTGCTTCCAAGGCTGTGGATTTGGCAGCAGGAGAGCTTCTTGAGGTTGCAACTCCTGGAAAAGgtttgcttct ... ttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttataaggaccatgcccatatatattttcctcatggctgtattttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA
                                         tatttttt  CT-rich tract
                   atatatattttcct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcttcttatttgacatattggatatttataaggaccatgcccatatatattttcctcatggctgtattttttgtgtagTTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG