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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcttttctgcacttacaaatattacttctccgcaacaaaaaaaacattcttttacaagatgaaatggacttgattttactttatgctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTCACTGCTGATGGTTTGCAAACTCTGACAAACAACTTGTGCTACAC

Basic information

species Oryza sativa
transcript LOC_Os02g45070.2
intron # 20
splice site 3'
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|218479705|gb|FG950878.1|FG950878
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GAAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|88960427|gb|CI006388.1|CI006388
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|86499428|gb|CI142061.1|CI142061
EST:     CCATCCTACTGAGTTTGATTTCTACCTGTGTAACCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: CCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|58673688|gb|CK062374.1|CK062374
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|86541213|gb|CI181419.1|CI181419
EST:     GCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACGAGTTC
genomic: GCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|14571449|gb|BI118817.1|BI118817
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|38469760|gb|CF953891.1|CF953891
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|86430935|gb|CI083358.1|CI083358
EST:     TGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCAGGTTCTGTGGGATGAGAACAAGTTC
genomic: TGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|218488951|gb|FG960688.1|FG960688
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|14571456|gb|BI118824.1|BI118824
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|29669480|gb|CB665755.1|CB665755
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|58599567|gb|CK010095.1|CK010095
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|29657069|gb|CB653344.1|CB653344
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|86521035|gb|CI161241.1|CI161241
EST:     GCCATCCTACTGAGTGTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
EST: gi|29626579|gb|CB631590.1|CB631590
EST:     GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG                         GGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC
genomic: GCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTC

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: 67 (upstream exon), 74 (downstream exon)
Score: 24

GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAGgtcagctttt ... ctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTCACTGCTGATGGTTTGCAAACTCTGACAAACAACTTGTGCTACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacattcttttacaagatgaaatggacttgattttactttatgctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTCACTGCTGATGGTTTGCAAACTCTGACAAACAACTTGTGCTACAC
                           acttgat  putative branch site (score: 24)
                                             ctattttt  putative PPT
                                attttactttatgcta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagcttttctgcacttacaaatattacttctccgcaacaaaaaaaacattcttttacaagatgaaatggacttgattttactttatgctatttttagGGAACAAGTCGCCCTGCACATTATCATGTTCTGTGGGATGAGAACAAGTTCACTGCTGATGGTTTGCAAACTCTGACAAACAACTTGTGCTACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT