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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGCTAATCTGACTGGAAACCCAGATCGCCTTCTTCGCTGGGGGTGGGGCGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgcctccctcctcctcctcctcctcctcctcactccttccggccccgatcctatagctcctccgctcgccgcggggatctgcttacgacgagg...

Basic information

species Oryza sativa
transcript LOC_Os01g51380.1
intron # 1
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|88352648|gb|CI624587.1|CI624587
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88724403|gb|CI747662.1|CI747662
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88433134|gb|CI569803.1|CI569803
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--G                         C-GGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88358211|gb|CI605136.1|CI605136
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGCTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88360936|gb|CI625242.1|CI625242
EST:     CGAAGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTG-G                         --GGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAA
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|163927702|gb|EG710506.1|EG710506
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGGGTCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88317359|gb|CI628008.1|CI628008
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88345261|gb|CI627902.1|CI627902
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88397163|gb|CI593375.1|CI593375
EST:     GCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: GCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88371072|gb|CI597549.1|CI597549
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTAAAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88360978|gb|CI625284.1|CI625284
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--G                         C-GGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|86901596|gb|CI310358.1|CI310358
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88356589|gb|CI626204.1|CI626204
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88724311|gb|CI747570.1|CI747570
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88314360|gb|CI604844.1|CI604844
EST:     GATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: GATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|88388263|gb|CI627802.1|CI627802
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--G                         C-GGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
EST: gi|66915737|gb|CX102585.1|CX102585
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAC

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: 52 (upstream exon), 60 (downstream exon)
Score: 12

ACCGCTAATCTGACTGGAAACCCAGATCGCCTTCTTCGCTGGGGGTGGGGCGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... ttacctacagCAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGCTAATCTGACTGGAAACCCAGATCGCCTTCTTCGCTGGGGGTGGGGCGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgcctccctcctcctcctcctcctcctcctcactccttccggccccgatcctatagctcctccgctcgccgcggggatctgcttacgacgagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC