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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAACTACATGCTGCGTCTCTTCTGCATTGGCTTCACCAAGAGGAGGCCAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaattgatgtatagttattttttctttatcaaattcaattgatgtatagttgttctgctattgttgagctgcttgtttatcgtgtttgattgtaatctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os12g21798.1
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|88969205|gb|CI382754.1|CI382754
EST:     CAGATTCGACAG                         ATCCCTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|33795240|gb|CF323492.1|CF323492
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGA
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGA
EST: gi|86512807|gb|CI155440.1|CI155440
EST:     CAAATCAAGTCGAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|88975405|gb|CI023656.1|CI023656
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|58684406|gb|CK073093.1|CK073093
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTG
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTG
EST: gi|88199744|gb|CI199594.1|CI199594
EST:     GCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: GCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|117216849|gb|CT845233.1|CT845233
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|86523196|gb|CI163402.1|CI163402
EST:     AAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: AAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|218498217|gb|FG958345.1|FG958345
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAA
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAA
EST: gi|58670980|gb|CK059666.1|CK059666
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGT
EST: gi|86494351|gb|CI136984.1|CI136984
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|66918188|gb|CX105036.1|CX105036
EST:     GCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGCTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: GCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|88832344|gb|CI019285.1|CI019285
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|11173097|gb|AU164611.1|AU164611
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|87032424|gb|CI264205.1|CI264205
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|86261132|gb|CI004697.1|CI004697
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|88240992|gb|CI240841.1|CI240841
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
EST: gi|38473073|gb|CF957205.1|CF957205
EST:     CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAG                         ATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT
genomic: CAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGAT

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: 74 (upstream exon), 72 (downstream exon)
Score: 36

TGATAACTACATGCTGCGTCTCTTCTGCATTGGCTTCACCAAGAGGAGGCCAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaa ... atctgtgcagATCCGTCGCAAGATGGTGGAGATCATGGTGAACCAGGCATCATCCTGTGATCTCAAGGAGCTGGTGTCAAAATTCATTCCTGAGGTGATTGGGAAGGAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAACTACATGCTGCGTCTCTTCTGCATTGGCTTCACCAAGAGGAGGCCAAATCAAGTCAAACGGACATGCTATGCTCAAGCAAGCCAGATTCGACAGgtaatttcaattgatgtatagttattttttctttatcaaattcaattgatgtatagttgttctgctattgttgagctgcttgtttatcgtgtttgattgtaatctgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG