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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgtcgccttcctgtaattttagttattttgtatatcttgttaaccctatgattgacacctcatttctttacctgaatttaatttctttatgttcatctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g45070.2
intron # 19
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:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|88960427|gb|CI006388.1|CI006388
EST:     ACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: ACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|58673688|gb|CK062374.1|CK062374
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|14571449|gb|BI118817.1|BI118817
EST:     TAACCACAGGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|38469760|gb|CF953891.1|CF953891
EST:     TAACCACAAGGACCAGCGCACTGTTNACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|58681274|gb|CK069961.1|CK069961
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|218488951|gb|FG960688.1|FG960688
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|14571456|gb|BI118824.1|BI118824
EST:     TAACCACAAGGACCAGCGCACCGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|29669480|gb|CB665755.1|CB665755
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|58599567|gb|CK010095.1|CK010095
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|29657069|gb|CB653344.1|CB653344
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|86521035|gb|CI161241.1|CI161241
EST:     GCACTGTTGACAGAAGTGGAAATATACTACCAG                         CCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTGTGATTTCTACC
genomic: GCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
EST: gi|29626579|gb|CB631590.1|CB631590
EST:     TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAG                         GCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC
genomic: TAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACC

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: 69 (upstream exon), 74 (downstream exon)
Score: 40

GTTACCTTTGTGGTGGTCCAGAAGCGTCATCACACAAGGCTGTTTGCTAATAACCACAAGGACCAGCGCACTGTTGACAGAAGTGGAAATATACTACCAGgtaatttgtc ... ctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacacctcatttctttacctgaatttaatttctttatgttcatctgatttcagGCACCGTGGTTGATTCAAAGATATGCCATCCTACTGAGTTTGATTTCTACCTGTGTAGCCATGCGGGCATTCAG
                                        ttcatct  CT-rich tract
                       aatttaatttctttat  TA-rich tract