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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcgccttatgcttcgttttttgaattgtaggtttttttattgatacttctgttcttcctaactttgtatgctaatttgagcctatggttgtgatgcagAATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAATTTTTGATGCTCGTGAAATATTGAGACTCACCAAGTTTGTGAGTCTAACC

Basic information

species Physcomitrella patens
transcript PP1S54_95V6.1
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|208386108|gb|DC949019.1|DC949019
EST:     TATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAG                         AATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAAT
genomic: TATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAGgtgagtatat ... tgtgatgcagAATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAAT
EST: gi|162205863|gb|FC381101.1|FC381101
EST:     TATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAG                         AATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAAT
genomic: TATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAGgtgagtatat ... tgtgatgcagAATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAAT
EST: gi|208396544|gb|DC915856.1|DC915856
EST:     TATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAG                         AATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAAT
genomic: TATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAGgtgagtatat ... tgtgatgcagAATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAAT

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: 29 (upstream exon), 29 (downstream exon)
Score: 4

TCCTCCTCCGAATCCTCCTCTTTCGCTTGCTCCAACTATGCAACATAGTGTATCAATAACTAAGGACGGAGTTCGAGAAGCACTTAATCGCCTCGTCAAGgtgagtatat ... tgtgatgcagAATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAATTTTTGATGCTCGTGAAATATTGAGACTCACCAAGTTTGTGAGTCTAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttctgttcttcctaactttgtatgctaatttgagcctatggttgtgatgcagAATGAGCATTTCATAGATATGGTGTACCGAGAGATGATGAATGCACACAATTTTTGATGCTCGTGAAATATTGAGACTCACCAAGTTTGTGAGTCTAACC
                            taatttga  TA-rich tract