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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgtgtggtacgtgttcttttggatcggtttgtgtggctctgtcaatgtatatcaacaacgattgacggttcttcttgtaatctttcgattactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTCTTGAAACCCGATGCCCCTGCTCCACAAATGCACGGAGTACGAACTTGGC

Basic information

species Physcomitrella patens
transcript PP1S28_304V6.1
intron # 10
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|162192562|gb|FC370609.1|FC370609
EST:     TACTGCTCAATTACATCGGTGGTGCCCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|67578799|gb|BJ950966.1|BJ950966
EST:     CTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGNCGGTGGATAAGGACCTCCGAACAATGCTC
genomic: CTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|162194557|gb|FC370780.1|FC370780
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|162186655|gb|FC363627.1|FC363627
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|162231097|gb|FC406208.1|FC406208
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|67694562|gb|BJ954795.1|BJ954795
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|162173588|gb|FC350162.1|FC350162
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|162155601|gb|FC331539.1|FC331539
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|162231096|gb|FC406207.1|FC406207
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
EST: gi|15327119|gb|BI487603.1|BI487603
EST:     TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAG                         AGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC
genomic: TACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTC

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: 22 (upstream exon), 31 (downstream exon)
Score: 8

CATTTACAGCTCCTCCTTATTTCCTAATCGGGCTCCAGAGGATCGTGTACTACTGCTCAATTACATCGGTGGTGCTCAATACCCACAAATTATGGAGAAGgtacatattg ... attactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTCTTGAAACCCGATGCCCCTGCTCCACAAATGCACGGAGTACGAACTTGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgtatatcaacaacgattgacggttcttcttgtaatctttcgattactgcagAGTGACGAGGAAATCGTGAAGACGGTGGATAAGGACCTCCGAACAATGCTCTTGAAACCCGATGCCCCTGCTCCACAAATGCACGGAGTACGAACTTGGC
                 gattgac  putative branch site (score: 8)
     tatatcaa  TA-rich tract