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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgattcacctcctgatttctctctgtttcgtttggaattgcttgataagtagcttcctgtgttggaatcagtgagatgcttgtaactgcaggatggatgatgacggatgttggggtatgtggtcggcgatcgctgtgtgtttgagttgtggagttaaggtgattaggtgtgtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTCTCAAGGGCAAGGGTGTGTACCAATTCGTAGACAAGTATGGTGCTAACGT

Basic information

species Physcomitrella patens
transcript PP1S54_166V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_166V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g10020.1 (Oryza sativa), 3'ss of exon 2
gtgagttgattcacctcctgatttctctctgtttcgtttggaattgcttgataagtagcttcctgtgttggaatcagtgagatgcttgtaactgcaggatggatgatgacggatgttggggtatgtggtcggcgatcgctgtgtgtttgagttgtggagttaaggtgattaggtgtgtttgtgcagGG---CCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTCTCAAGGGCAAGGGTGTGTACCAATTCGTAGACAAGTATGGTGCTAACGT------------
                                                                                                                                                 |   ||||   | |  ||  |     | | ||||  | ||  |   |||||||      ||   |   |      |||      |    ||    |  |||| |||||||||||||||||||| |||||||| || || |||||            
-------------------------------------------------------------------------------------------------------------------------------------------------tccaagtttcagtgacaatttcgcaggttttgttcattcaaagattccatctgtcagactatgcactgaataaactgacagatttttgtgatggatgcagGGGAAGGGTGTGTACCAATTCGTTGACAAGTACGGCGCAAACGTCGACGGCTACAG
















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|67577829|gb|BJ949996.1|BJ949996
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|162278888|gb|FC454939.1|FC454939
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|18326698|gb|BJ158697.1|BJ158697
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|162246108|gb|FC421919.1|FC421919
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTAG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|18334687|gb|BJ166704.1|BJ166704
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|162244664|gb|FC420133.1|FC420133
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTAG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|162242528|gb|FC419196.1|FC419196
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTAG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
EST: gi|162244665|gb|FC420134.1|FC420134
EST:     CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTAG                         GGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC
genomic: CTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTC

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: 35 (upstream exon), 35 (downstream exon)
Score: 119

GTTGCTGTGCAGGGAGTAACCCCCCTCAGCCTCTCCAGAACCTCCCGCTCCTTGATCGTCACTGCTAGCACGAAGAAGATCAAGGTTTCTCAACCACTGGgtgagttgat ... gtttgtgcagGGCCATCTGGAGACTTAAAGAAGAAGGGTGTTGATGCTGGTGGCCGAGTTCTCAAGGGCAAGGGTGTGTACCAATTCGTAGACAAGTATGGTGCTAACGT




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