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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtaactagcatgacaacacccagagcaatatacagatcaatgagctttttacattttgcctactctatataacttgaactagcactatattgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g44220.6
intron # 10
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|116875182|gb|EC365690.1|EC365690
EST:     ACTTTGAATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|88461656|gb|CI695498.1|CI695498
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|2797455|gb|AA750749.1|AA750749
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|29680979|gb|CB677254.1|CB677254
EST:     AGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: AGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|116875001|gb|EC365509.1|EC365509
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|66915625|gb|CX102473.1|CX102473
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|29668852|gb|CB665127.1|CB665127
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|116875027|gb|EC365535.1|EC365535
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
EST: gi|1631864|gb|C19593.1|C19593
EST:     ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG                         GCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT
genomic: ACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTT

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), 75 (downstream exon)
Score: 341

GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAGgtaagttccg ... attgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttttacattttgcctactctatataacttgaactagcactatattgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG
                       atataac  putative branch site (score: 341)
                                              ttgtttt  putative PPT
                                        actatattgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtaactagcatgacaacacccagagcaatatacagatcaatgagctttttacattttgcctactctatataacttgaactagcactatattgttttagGCATGTGTCTTCACAGAATATTGGGAGGATATTGGAACAATCAAATCATTTTTTGATGCTAACTTGGCCCTCACCGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - -gcatgac
- - - - - - - - - - - - -agcaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctac