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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatgctaattacttaatttttggctgtttttgttgagggaggtttgcgtttttcgtggatattgattttctggttaatgttaactcatgtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCTTCAAGTGGAACCAAACATGCTTCATTCCCCCAAGCCATTGATGTCCACC

Basic information

species Oryza sativa
transcript LOC_Os01g20110.1
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|29656601|gb|CB652876.1|CB652876
EST:     ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAG                         GCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCT
genomic: ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAGgtctggtcct ... gtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCT
EST: gi|58689419|gb|CK078106.1|CK078106
EST:     ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAG                         GCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCGATCT
genomic: ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAGgtctggtcct ... gtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCT
EST: gi|58683301|gb|CK071988.1|CK071988
EST:     ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAG                         GCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCGATCT
genomic: ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAGgtctggtcct ... gtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCT
EST: gi|88348425|gb|CI639084.1|CI639084
EST:     ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAG                         GCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCT
genomic: ACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAGgtctggtcct ... gtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCT

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: 20 (upstream exon), 71 (downstream exon)
Score: 6

CAGCCACGCGGCAGGCTCCTCGCTGCCCCCCGGCTGCCGCCGCGCCGCCGACCCATGGCTACCGGCGTGGAGCCGCGGTGCTCTCCGGCCGCCGGGGAAGgtctggtcct ... gtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCTTCAAGTGGAACCAAACATGCTTCATTCCCCCAAGCCATTGATGTCCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgtttttcgtggatattgattttctggttaatgttaactcatgtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCTTCAAGTGGAACCAAACATGCTTCATTCCCCCAAGCCATTGATGTCCACC
                                  tgttaac  putative branch site (score: 6)
                                            tgtttct  putative PPT
               atattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatgctaattacttaatttttggctgtttttgttgagggaggtttgcgtttttcgtggatattgattttctggttaatgttaactcatgtttctgcagGCATACTTTGAGTTCAATACAATTGATGCATGCTGTTAGAGGTGGCAATCTTCAAGTGGAACCAAACATGCTTCATTCCCCCAAGCCATTGATGTCCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
agcatgc
- - - - - - - - - - - -ggctgtt
- - - - - - - - - - - - - - - -ttgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttctg