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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatattatgtaattacttacatggaaatgtcacctctgcttgacatatagtttcagttaggtgacatttcatcactatagctagtctgcagaattttgatgggctggatggtatctcatgtttcag

Basic information

species Oryza sativa
transcript LOC_Os06g24070.1
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|33669836|gb|CF298075.1|CF298075
EST:     ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|16577914|gb|BI812009.1|BI812009
EST:     GCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGC
genomic: GCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|86851181|gb|CI312582.1|CI312582
EST:     TGCCAACTCAAAGGGGACACCTTGCATGGCGATGCCCCATGCCAGTTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: TGCCAACTC-AA-GGGACACCTTGCATGGCGATG-CCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|29646518|gb|CB651525.1|CB651525
EST:     ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|29677764|gb|CB674039.1|CB674039
EST:     ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|87015668|gb|CI277626.1|CI277626
EST:     ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|88971522|gb|CI017836.1|CI017836
EST:     TGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: TGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|38474383|gb|CF958515.1|CF958515
EST:     ATGTGCCAACTCAATGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|58689120|gb|CK077807.1|CK077807
EST:     AAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: AAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|88967370|gb|CI002522.1|CI002522
EST:     ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
EST: gi|22306077|gb|BQ907299.1|BQ907299
EST:     ATGTGCCAACTCAAGGGACACCTTGCAT-GCGATGCCCATGCCAGCTGCG                         AGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG
genomic: ATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGG

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: 51 (upstream exon), 73 (downstream exon)
Score: 9

GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatatt ... catgtttcagAGATTTCCTGCTCCACCGGTGCCAGGAGTTGTCCCGTGTCCAATGTATAGGCCATTGACTCCACCAGCACTGGCGAGCAAGAATCAGCAGGACGCACAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCGgtaagatattatgtaattacttacatggaaatgtcacctctgcttgacatatagtttcagttaggtgacatttcatcactatagctagtctgcagaattttgatgggctggatggtatctcatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC