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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATTCATGGCGAGGTTGGTGTCGACCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgagactctcttgccgcgtcctcttaatcgatagtttggtgcattttgtctgccttgtctgttcattgaggtgattctgtaatgtaattactcca...

Basic information

species Oryza sativa
transcript LOC_Os01g07950.1
intron # 2
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|33687689|gb|CF315928.1|CF315928
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88352871|gb|CI678899.1|CI678899
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88448599|gb|CI693990.1|CI693990
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88371997|gb|CI681514.1|CI681514
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|87006043|gb|CI289460.1|CI289460
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88367351|gb|CI566317.1|CI566317
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88337404|gb|CI629694.1|CI629694
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88331903|gb|CI642128.1|CI642128
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTT
EST: gi|88327320|gb|CI645097.1|CI645097
EST:     CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCT                         GTATGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGG
genomic: CCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagG----CTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGG

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: 66 (upstream exon), 74 (downstream exon)
Score: 12

GGGATTCATGGCGAGGTTGGTGTCGACCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgaga ... ggaataatagGCTGTGTCACAACCAGCTATCCAGCAGTTTAGGAACTACTCACCAGGACTTGGTGGTGATTCTAGAGGAAGTGGGGACTCAAGTTCAACACGAGTAGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATTCATGGCGAGGTTGGTGTCGACCGCTCTCATGAGAGGGCTCGTGAGATCGAGCCGCGCGCCGAGAGTAGCTgtatgtgagactctcttgccgcgtcctcttaatcgatagtttggtgcattttgtctgccttgtctgttcattgaggtgattctgtaatgtaattactcca

- - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcgtcc