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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctagtcagtggtcatcactattatggcaatagaccgtcgttcagctttttacccttagttgtgaatctctaactattcagctttgttgggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGACATTTCTTCTACTGCCAAGAAGATCATTTCATCACCCCTTACACTGGCA

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 11
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|88264876|gb|CI367527.1|CI367527
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88906152|gb|CI375224.1|CI375224
EST:     GTCGTAGCATCTGAAGACATAGGGA-GCAGATTTTGACGTAT-GGGAAA-                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCTCCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|89191950|gb|CI250891.1|CI250891
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCGTTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88838739|gb|CI376277.1|CI376277
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88964180|gb|CI045373.1|CI045373
EST:     GTCGTAGCATCTGAAGACATAGGGAGCCAGATTTTGACGTATGGGGAAAG                         GAAACCCCTTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|89166280|gb|CI103370.1|CI103370
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88834759|gb|CI370062.1|CI370062
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88250927|gb|CI248778.1|CI248778
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|5701695|gb|AU063482.2|AU063482
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|86893269|gb|CI313403.1|CI313403
EST:     TCGTAGCATCTGAAGACATAGGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: TCGTAGCATCTGAAGACATA-GGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88267554|gb|CI379489.1|CI379489
EST:     GAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|86593940|gb|CI260169.1|CI260169
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88268173|gb|CI377910.1|CI377910
EST:     TCGTAGCATCTGAAGACATAGGGA-GCAGATTTTGACGTAT-GGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: TCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|38475250|gb|CF959383.1|CF959383
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCAC
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCAC
EST: gi|88843303|gb|CI372203.1|CI372203
EST:     GGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|9864980|gb|AU100730.1|AU100730
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|86841142|gb|CI342900.1|CI342900
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88297257|gb|CI545347.1|CI545347
EST:     CGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: CGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|86434084|gb|CI094427.1|CI094427
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCGCCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|87021256|gb|CI295315.1|CI295315
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88436304|gb|CI519223.1|CI519223
EST:     CATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: CATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|88967984|gb|CI098226.1|CI098226
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|58597827|gb|CK008355.1|CK008355
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
EST: gi|163920798|gb|EG710061.1|EG710061
EST:     GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG                         GAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA
genomic: GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGA

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), 73 (downstream exon)
Score: 15

GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAGgtatggttgc ... gggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGACATTTCTTCTACTGCCAAGAAGATCATTTCATCACCCCTTACACTGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttttacccttagttgtgaatctctaactattcagctttgttgggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGACATTTCTTCTACTGCCAAGAAGATCATTTCATCACCCCTTACACTGGCA
                        ctctaac  putative branch site (score: 15)
                           taactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctagtcagtggtcatcactattatggcaatagaccgtcgttcagctttttacccttagttgtgaatctctaactattcagctttgttgggatcgcagGAAACCCATTGAGCATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGACATTTCTTCTACTGCCAAGAAGATCATTTCATCACCCCTTACACTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatc