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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctccctcctctggcaccctgccatcttgtgcctgcgctactacctcatccaccgaatttgaccattggtccctgtttgttgctggtttgctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACCGCGCTGCTGAGAAGGCTGTTCACGAGGAGTGACGGTAGCAAGGAGTCGA

Basic information

species Oryza sativa
transcript LOC_Os02g28980.1
intron # 11
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|29665077|gb|CB661352.1|CB661352
EST:     ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|29634035|gb|CB639044.1|CB639044
EST:     ACTCGGAAACCGAA                         GGAGGCACAATTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|88995058|gb|CI036633.1|CI036633
EST:     GATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: GATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|218501934|gb|FG968124.1|FG968124
EST:     ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|88964074|gb|CI032991.1|CI032991
EST:     ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|86534923|gb|CI175129.1|CI175129
EST:     ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTTGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|29644965|gb|CB649972.1|CB649972
EST:     ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|86831259|gb|CI297528.1|CI297528
EST:     ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: ACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
EST: gi|88849488|gb|CI089396.1|CI089396
EST:     GATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAA                         GGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC
genomic: GATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACC

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: 75 (upstream exon), 66 (downstream exon)
Score: 12

GAGGCTGAAGGAGAAGGTCAAGGAGCAGAAGAGGAAGGAAACGAAATTGTACGGCAACATGATTTCGAAGCTAAGCAAGCTTGAAGACTCGGAAACCGAAgtaagctccc ... ctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACCGCGCTGCTGAGAAGGCTGTTCACGAGGAGTGACGGTAGCAAGGAGTCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatccaccgaatttgaccattggtccctgtttgttgctggtttgctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACCGCGCTGCTGAGAAGGCTGTTCACGAGGAGTGACGGTAGCAAGGAGTCGA
           atttgac  putative branch site (score: 12)
          aatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctccctcctctggcaccctgccatcttgtgcctgcgctactacctcatccaccgaatttgaccattggtccctgtttgttgctggtttgctgcttgaagGGAGGCACAACTCAGGCGCCAAGCAAGAAGCATGGCCTATGGCCACTCACCGCGCTGCTGAGAAGGCTGTTCACGAGGAGTGACGGTAGCAAGGAGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG