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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCTATCGCATACCATCAGCCTAGTCCATTGCCAAGGCCAAATGGAAAGGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaacacatcatctgtccatccacccaatctgttggatgcgagcccatctctaacttctgatccctgtactgccag

Basic information

species Oryza sativa
transcript LOC_Os03g55560.2
intron # 11
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|88455705|gb|CI524124.1|CI524124
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|86481716|gb|CI124349.1|CI124349
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|86481866|gb|CI124499.1|CI124499
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|29615115|gb|CB620128.1|CB620128
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|88268958|gb|CI380256.1|CI380256
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|2317517|gb|C22571.1|C22571
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|29661683|gb|CB657958.1|CB657958
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|88219023|gb|CI220583.1|CI220583
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGATCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|86489197|gb|CI131830.1|CI131830
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|88289096|gb|CI520426.1|CI520426
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|2317515|gb|C22569.1|C22569
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
EST: gi|2317465|gb|C22519.1|C22519
EST:     GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAG                         TCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG
genomic: GGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAG

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: 56 (upstream exon), 61 (downstream exon)
Score: 4

TTTTCTATCGCATACCATCAGCCTAGTCCATTGCCAAGGCCAAATGGAAAGGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaac ... gtactgccagTCATCATAATTGAACATTCGCTGGGTCTTGTAAAGTACTTGGCATGCGAAGGACATCAGCACGGTACGATCGCAATAGCTTCTGAAACCTGTAATGTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCTATCGCATACCATCAGCCTAGTCCATTGCCAAGGCCAAATGGAAAGGAAGCAATAAATTTGTTCACCTTGAAGCATGACGAGCTGCCTACCTAAGgtgcggaaacacatcatctgtccatccacccaatctgttggatgcgagcccatctctaacttctgatccctgtactgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC