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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggtcaaagatgctaggttggtgttttcacctcgaatatacaactgtaccctaatgttttgctgttgtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAATATACGATTCTTTATGCTTCTCAGCCCTTTGGTTTGCTAGAGAACCCTTC

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
intron # 7
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|29613045|gb|CB618058.1|CB618058
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGACTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|33689369|gb|CF317608.1|CF317608
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|88239758|gb|CI238920.1|CI238920
EST:     GTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: GTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29658171|gb|CB654446.1|CB654446
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29672707|gb|CB668982.1|CB668982
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|8856727|gb|AU094045.1|AU094045
EST:     TCTGATTGTCTTCTGTGATGGTGNTTTCAAGGATAACNCAAATTCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29663528|gb|CB659803.1|CB659803
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGGAGCTAA-
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGG-AGCTAAA
EST: gi|29678425|gb|CB674700.1|CB674700
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29658170|gb|CB654445.1|CB654445
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|86422104|gb|CI059677.1|CI059677
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29678424|gb|CB674699.1|CB674699
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTANAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|27545747|gb|CA763944.2|CA763944
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGACTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29663529|gb|CB659804.1|CB659804
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|87016616|gb|CI275618.1|CI275618
EST:     GGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: GGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29672708|gb|CB668983.1|CB668983
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT
EST: gi|29624905|gb|CB629916.1|CB629916
EST:     TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAG                         GGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGACTGGAGCTAAAT
genomic: TCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAAT

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: 72 (upstream exon), 40 (downstream exon)
Score: 15

GGATTGGTGGCATCACAAACTAAAAAGAACCCGAGTGGACAGACTGATCTGATTGTCTTCTGTGATGGTGGTTTCAAGGATAACACAAAATCAGAAGgttaggtcaa ... gtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAATATACGATTCTTTATGCTTCTCAGCCCTTTGGTTTGCTAGAGAACCCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcacctcgaatatacaactgtaccctaatgttttgctgttgtttctgtagGGGAGTTGCTTTCTGAGCTGGTTACTCTGCTGAAGAAGTCTGGAGCTAAATATACGATTCTTTATGCTTCTCAGCCCTTTGGTTTGCTAGAGAACCCTTC
                           ccctaat  putative branch site (score: 15)
                                           ttgtttct  putative PPT
             aatatacaa  TA-rich tract