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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_Os01g51380.2
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|88360936|gb|CI625242.1|CI625242
EST:     CGAAGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGGG                         GCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGAAACG
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
EST: gi|88356589|gb|CI626204.1|CI626204
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88433134|gb|CI569803.1|CI569803
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         GCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
EST: gi|88352648|gb|CI624587.1|CI624587
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|86901596|gb|CI310358.1|CI310358
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88345261|gb|CI627902.1|CI627902
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88724403|gb|CI747662.1|CI747662
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|66915737|gb|CX102585.1|CX102585
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88388263|gb|CI627802.1|CI627802
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         GCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
EST: gi|88317359|gb|CI628008.1|CI628008
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|58672899|gb|CK061585.1|CK061585
EST:     TCGAATCTGCG                         GCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
genomic: TCGAATCTGCGgtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
EST: gi|88358211|gb|CI605136.1|CI605136
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88371072|gb|CI597549.1|CI597549
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|163927702|gb|EG710506.1|EG710506
EST:     CGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGGGTCTGCGCAG                         GCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACAC
genomic: CGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACAC
EST: gi|88314360|gb|CI604844.1|CI604844
EST:     GATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: GATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88360978|gb|CI625284.1|CI625284
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCG                         GCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACG
EST: gi|88397163|gb|CI593375.1|CI593375
EST:     GCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: GCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc
EST: gi|88724311|gb|CI747570.1|CI747570
EST:     CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGCAG                       
genomic: CGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCT--GC-Ggtacgcacgc ... cctacagc

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), 75 (downstream exon)
Score: 6

ACCGCTAATCTGACTGGAAACCCAGATCGCCTTCTTCGCTGGGGGTGGGGCGACGAAACTTGCGCGATCTCCCCTCTCCTCTCCTCCGCTCGAATCTGCGgtacgcacgc ... cctacagcagGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG




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

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