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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACAGGCAGGGGCCTGGACCTGCATATGGAGGAGATAACTGGCAAGGGGGTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagcatttggtatatgattatttactggtaaacttattattttgaagagacaatttagtttacacctattggtatttgtgcatcatgaatcaat...

Basic information

species Oryza sativa
transcript LOC_Os11g11020.1
intron # 4
splice site 5'
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|88470769|gb|CI408040.1|CI408040
EST:     GTTCTAATCAGTATCCTAGCCCAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATNTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|86867264|gb|CI337782.1|CI337782
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGCCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|33688862|gb|CF317101.1|CF317101
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCA
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGG-AAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCA
EST: gi|86544077|gb|CI184283.1|CI184283
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|87029420|gb|CI250353.1|CI250353
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|86854011|gb|CI252002.1|CI252002
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATGAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|89188271|gb|CI115520.1|CI115520
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|66919085|gb|CX105933.1|CX105933
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|88503479|gb|CI430985.1|CI430985
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
EST: gi|86477579|gb|CI120212.1|CI120212
EST:     GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGG                         GGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT
genomic: GTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCAT

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: 68 (upstream exon), 73 (downstream exon)
Score: 29

CAACAGGCAGGGGCCTGGACCTGCATATGGAGGAGATAACTGGCAAGGGGGTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagc ... gtgtttgcagGGAAGGCAATAAGGGCTTTAACATGTGTTCCAGTCACGGACGAGAGGGCATAATTATGCTGCTTGAAATGTAGAAACTCCCACCTGTACAATAAATGACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACAGGCAGGGGCCTGGACCTGCATATGGAGGAGATAACTGGCAAGGGGGTTCTAATCAGTATCCTAGCCAAAGCGAAGGACAACAAGAGAGCTGGCGGgtaagaaagcatttggtatatgattatttactggtaaacttattattttgaagagacaatttagtttacacctattggtatttgtgcatcatgaatcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT