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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctacattaccacttgtgttcttattgttatagtggtgttaatgatatattatattattgtgatttgttttgctaaacagcatcatctgcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGTTGAAGTTGCACCTACCTCTGTCTCAGTCTCAGAGGGGAAATCTGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os04g52960.1
intron # 1
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|88305288|gb|CI653012.1|CI653012
EST:     GCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: GCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|58692865|gb|CK081552.1|CK081552
EST:     CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|218494329|gb|FG970076.1|FG970076
EST:     GTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTGCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGGAAGTCAAGCAAGAAATCTGCTGT
genomic: GTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|29633107|gb|CB638116.1|CB638116
EST:     CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|86888434|gb|CI303716.1|CI303716
EST:     CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|88349407|gb|CI621517.1|CI621517
EST:     CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|88341180|gb|CI639937.1|CI639937
EST:     TTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTACGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: TTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|88364704|gb|CI612519.1|CI612519
EST:     CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATAGTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|88358345|gb|CI606854.1|CI606854
EST:     CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
genomic: CAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT
EST: gi|58662979|gb|CK051665.1|CK051665
EST:     GCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGG                         AATTAATTAAGCAATACTTAATATGGGGAAGTCAAGCAAGAAATCTGCTGT
genomic: GCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGT

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: 64 (upstream exon), 67 (downstream exon)
Score: 19

ACCTCGAGCCCCCAGGTCCGCCTCGCCTCTCCGTCGCTTGCCGCCGCCCGCAGTGGTCGCCGGCCGCGCGGGGCTTCGCCGGTGTCGCTTCCTCGTTTGGgtaagtcgct ... gcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGTTGAAGTTGCACCTACCTCTGTCTCAGTCTCAGAGGGGAAATCTGGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatattatattattgtgatttgttttgctaaacagcatcatctgcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGTTGAAGTTGCACCTACCTCTGTCTCAGTCTCAGAGGGGAAATCTGGGAAG
                           tgctaaa  putative branch site (score: 19)
                                          tctgctttt  putative PPT
     attatattattgtgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctacattaccacttgtgttcttattgttatagtggtgttaatgatatattatattattgtgatttgttttgctaaacagcatcatctgcttttgtagAATTAATTAAGCAATACTTAATATGGGCAAGTCAAGCAAGAAATCTGCTGTTGAAGTTGCACCTACCTCTGTCTCAGTCTCAGAGGGGAAATCTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
-tcctaca
- - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - -tggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcatc