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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtacctttttgacccactttagtttttttttcttggtgcagacagtcatcatgagcatgttggtttaatggcttctaaaatatttaacccgcatccacatttcctgagtgtgaatttgtttctacattgtttaattcctttacattttacttcttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG

Basic information

species Oryza sativa
transcript LOC_Os02g56210.1
intron # 6
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|218489304|gb|FG963268.1|FG963268
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|66916903|gb|CX103751.1|CX103751
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|86886462|gb|CI322694.1|CI322694
EST:     TCTCGTGGAGTGAATGGGAGGAAGCTCTATATGGTCGCACCATTGTTCCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|88269261|gb|CI380559.1|CI380559
EST:     TGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|218495675|gb|FG954247.1|FG954247
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|25803115|gb|CA759076.1|CA759076
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|218484683|gb|FG956662.1|FG956662
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGAATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|86433955|gb|CI094298.1|CI094298
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|86593586|gb|CI264465.1|CI264465
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|88906305|gb|CI375377.1|CI375377
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCT-GATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
EST: gi|218481891|gb|FG948637.1|FG948637
EST:     TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGTTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATC
genomic: TCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATC
EST: gi|88490387|gb|CI427659.1|CI427659
EST:     GTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCA                         GGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC
genomic: GTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATC

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), 70 (downstream exon)
Score: 49

TCTCATGGCACAACATCGATGAACTCCTTCCTGCTGGTGATGACGCAATATCTCGTGGAGTGAATGGGATGAAGCTCTATATGGTCGCACCATTTTTGCAgtcagtacct ... cttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgaatttgtttctacattgtttaattcctttacattttacttcttcatccagGGGTCTAAAAGCCTGGATAGCCACACATCGTCACCCACAGTATCAGAAATCAGACACGTCTGCTAGAG
                     gtttaat  putative branch site (score: 49)
                           ttcctttacattttac  CT-rich tract
               tacattgtttaatt  TA-rich tract