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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCCTTTCAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcgccgctcatcttaacattgtacagcttcataggcttccagttgggaaggagtttgtggttgcttgtgcaattccttgtgggagatggtctgtccaaagttcttccccctaaacgggaggcgatctagttctcctgaggggtgtgcatggttgttgatgtatactaagtttttggtcatcaccactcag

Basic information

species Physcomitrella patens
transcript PP1S47_277V6.1
intron # 1
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|18349800|gb|BJ181850.1|BJ181850
EST:     ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|208380153|gb|DC927432.1|DC927432
EST:     ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67698997|gb|BJ959230.1|BJ959230
EST:     GTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|208396407|gb|DC920073.1|DC920073
EST:     TCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: TCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|162258306|gb|FC434233.1|FC434233
EST:     CTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: CTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|100374751|gb|BY949051.1|BY949051
EST:     ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|18369192|gb|BJ201277.1|BJ201277
EST:     GGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|37845862|gb|BJ603870.1|BJ603870
EST:     TGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: TGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67717319|gb|BJ967578.1|BJ967578
EST:     ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|208352405|gb|DC906188.1|DC906188
EST:     TCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: TCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|208349966|gb|DC913674.1|DC913674
EST:     ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|18353103|gb|BJ185158.1|BJ185158
EST:     CAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: CAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|18358961|gb|BJ191021.1|BJ191021
EST:     GGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|162237414|gb|FC412717.1|FC412717
EST:     CTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: CTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67575789|gb|BJ948613.1|BJ948613
EST:     AGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: AGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|18371408|gb|BJ203010.1|BJ203010
EST:     GTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|18368948|gb|BJ201033.1|BJ201033
EST:     GTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67575451|gb|BJ948275.1|BJ948275
EST:     C-ACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: CAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67725836|gb|BJ976095.1|BJ976095
EST:     ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: ATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67702984|gb|BJ963217.1|BJ963217
EST:     CAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACAGACATTTCAA
genomic: CAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|18361266|gb|BJ193331.1|BJ193331
EST:     GTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67698918|gb|BJ959151.1|BJ959151
EST:     CAA-CTTCCNTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: CAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
EST: gi|67695614|gb|BJ955847.1|BJ955847
EST:     GTCTTGTCTCTGGAGCGTCTCGAAG                         GGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA
genomic: GTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAA

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: 33 (upstream exon), 35 (downstream exon)
Score: 38

ATGCCCTTTCAACCTCCCTTGCTCCATTCGGTGTGTCTTGTCTCTGGAGCGTCTCGAAGgtgtgcctcg ... caccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAAGAAGGACTGGCAAAACTATGTGAGGACGTGGTTCAACCAGCCCGCTCGC




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