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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCTGCACCAATGGCGCCTTCGGTGCATCGTCACCGGGAGGCAACGCCGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagcactgcacaccttggtgtctccatccatcttcaatggatctatctttgcaatcatgcattcagtcttgacagctacatctttccatactatt...

Basic information

species Oryza sativa
transcript LOC_Os11g29840.1
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|86497910|gb|CI140543.1|CI140543
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|29660472|gb|CB656747.1|CB656747
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|86503509|gb|CI146142.1|CI146142
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|86502350|gb|CI144983.1|CI144983
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|88223842|gb|CI223691.1|CI223691
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|88989272|gb|CI043771.1|CI043771
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|29641691|gb|CB646698.1|CB646698
EST:     CGAGATGAACGGCAACAAGAGCGGCCCCTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|88198427|gb|CI198277.1|CI198277
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|89177380|gb|CI250829.1|CI250829
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
EST: gi|87037435|gb|CI192057.1|CI192057
EST:     CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACT                         ACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT
genomic: CGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCAT

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: 43 (upstream exon), 33 (downstream exon)
Score: 3

GGCTGCTGCACCAATGGCGCCTTCGGTGCATCGTCACCGGGAGGCAACGCCGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagca ... tctgatgcagACTTGGTGCTGGAATTATAATGGGGAAAAGAAGAGGAGCTATTTGTTTCATCAAGAATTAAAGCTTGAATAGTGAGCATCTCATATATATGAATATGTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGCTGCACCAATGGCGCCTTCGGTGCATCGTCACCGGGAGGCAACGCCGAGATGAACGGCAACAAGAGCGGCCACTGGATCAAGACTGATGCCGACTgtgagtagcactgcacaccttggtgtctccatccatcttcaatggatctatctttgcaatcatgcattcagtcttgacagctacatctttccatactatt

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccatcc