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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcacccatttgtgatagttcggtccacttcctatgtcttctgataattcgtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g44220.5
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|116875182|gb|EC365690.1|EC365690
EST:     TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAA                         GTCAAAATATGCACACCTGCAAGACTTTGAATCAGAAATTCTCCCGAGAGC
genomic: TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
EST: gi|88461656|gb|CI695498.1|CI695498
EST:     TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAA                         GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
genomic: TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
EST: gi|2797455|gb|AA750749.1|AA750749
EST:     CTTGAAAAAGGATGTTCTTTTAGACATTCTGAA                         GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
genomic: CTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
EST: gi|116875001|gb|EC365509.1|EC365509
EST:     TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGGA                         GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
genomic: TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
EST: gi|66915625|gb|CX102473.1|CX102473
EST:     TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAA                         GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
genomic: TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
EST: gi|116875027|gb|EC365535.1|EC365535
EST:     TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAA                         GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
genomic: TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
EST: gi|1631864|gb|C19593.1|C19593
EST:     TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAA                         GTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC
genomic: TCAATGGGAATTTATGTCTTGAAAAAGGATGTTCTTTTAGACATTCTGAAgtaagtgtca ... gtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttgtgatagttcggtccacttcctatgtcttctgataattcgtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG
                                 ttctgat  putative branch site (score: 3)
                                              tattctt  putative PPT
                                    tgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcacccatttgtgatagttcggtccacttcctatgtcttctgataattcgtattcttagGTCAAAATATGCACACCTGCAAGACTTTGGATCAGAAATTCTCCCGAGAGCTGTTTTAGAGCATAATGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA