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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATTGCAACGAGGCAAAATTATGTGCGCTTGGTTGAATCGGTAAAAAAATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattcgtatccatttgtacttcactataactgctcatcaaaatgcaatagaccagttcataaataattgtcacattttcatattaacctttttgaacaaggaatttattaatttgtaatttgcattagtttgctgcattgtgttctctgtgtttaaggtggatttttttttttcatttgagcag

Basic information

species Oryza sativa
transcript LOC_Os04g56480.3
intron # 14
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|89182762|gb|CI114131.1|CI114131
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86883503|gb|CI338061.1|CI338061
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88224189|gb|CI224038.1|CI224038
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88428005|gb|CI556899.1|CI556899
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88429886|gb|CI562697.1|CI562697
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86505661|gb|CI148294.1|CI148294
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88457668|gb|CI539464.1|CI539464
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86840851|gb|CI335043.1|CI335043
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86600311|gb|CI356068.1|CI356068
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86864162|gb|CI334008.1|CI334008
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88296986|gb|CI542698.1|CI542698
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88446697|gb|CI526530.1|CI526530
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86257435|gb|CI004252.1|CI004252
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86825581|gb|CI361755.1|CI361755
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86505390|gb|CI148023.1|CI148023
EST:     TGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: TGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88544532|gb|CI472636.1|CI472636
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88227542|gb|CI227022.1|CI227022
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88286498|gb|CI524997.1|CI524997
EST:     TTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: TTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86854586|gb|CI258879.1|CI258879
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG

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: 71 (upstream exon), 74 (downstream exon)
Score: 33

GACATTGCAACGAGGCAAAATTATGTGCGCTTGGTTGAATCGGTAAAAAAATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAGATTTAGAGGACATTGAGATGTGATAATTCCACCGTTCAGAATTGGCAAT




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