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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCCTCAGCGTCGAGTACCACCCGCGGAACCCCACGAGGAGCCCCGTACAAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagcaaccatttaatcccttttctgaatttttgtacgacgcaggcagaacaatgaaattattgaggtcccctagcaattaagattgatgggttgg...

Basic information

species Oryza sativa
transcript LOC_Os01g15120.1
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|218495743|gb|FG944638.1|FG944638
EST:     AAACCCTCAGGCCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAG                         AAACCTGGAGTGNCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
genomic: AAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
EST: gi|88691185|gb|CI735264.1|CI735264
EST:     GGGGACGGCCACTACATCTGCTTCTTCCAG                         AAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
genomic: GGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
EST: gi|29686898|gb|CB683173.1|CB683173
EST:     AAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAG                         AAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
genomic: AAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
EST: gi|88688202|gb|CI731778.1|CI731778
EST:     GGGGACGGCCACTACATCTGCTTCTTCCAG                         AAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
genomic: GGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
EST: gi|3763601|gb|AU030353.1|AU030353
EST:     AAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAG                         AAACCTGGNGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
genomic: AAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
EST: gi|88689305|gb|CI732881.1|CI732881
EST:     GGGGACGGCCACTACATCTGCTTCTTCCAG                         AAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC
genomic: GGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTC

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), 75 (downstream exon)
Score: 14

CGCCCTCAGCGTCGAGTACCACCCGCGGAACCCCACGAGGAGCCCCGTACAAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagca ... atgtgtgcagAAACCTGGAGTGGCCGAAGCTGAATTTGGTAGAGGTGATATAAAGTGTCTCTTGAAGAAATTCTATGGAATGCGCAAGGCAGCACCTCTGATTATACCCC




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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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCCTCAGCGTCGAGTACCACCCGCGGAACCCCACGAGGAGCCCCGTACAAACCCTCAGGGCCGTGTGCGGGGACGGCCACTACATCTGCTTCTTCCAGgtgaacagcaaccatttaatcccttttctgaatttttgtacgacgcaggcagaacaatgaaattattgaggtcccctagcaattaagattgatgggttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctagc