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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagaatcccccgctcttgactcaagtcacgaagtctcaagctttaggtgcatgtacgttcgcaatgactgaaatctaacttggaaaactggactgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG

Basic information

species Physcomitrella patens
transcript PP1S46_325V6.1
intron # 3
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|208349859|gb|DC905983.1|DC905983
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|100387711|gb|BY951711.1|BY951711
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|18349970|gb|BJ182021.1|BJ182021
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|18356177|gb|BJ188236.1|BJ188236
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCT-TATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|37833115|gb|BJ591127.1|BJ591127
EST:     CTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCT-TATG
genomic: CTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|18348858|gb|BJ180907.1|BJ180907
EST:     TATACTTAAAAGCTGGAGTGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|208387810|gb|DC941379.1|DC941379
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|208393393|gb|DC942491.1|DC942491
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|162269338|gb|FC444816.1|FC444816
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|208379946|gb|DC927672.1|DC927672
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|18346616|gb|BJ178661.1|BJ178661
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|208353247|gb|DC913921.1|DC913921
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|162269339|gb|FC444817.1|FC444817
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|208363225|gb|DC954383.1|DC954383
EST:     ATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: ATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|15327526|gb|BI488280.1|BI488280
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
EST: gi|208344704|gb|DC905153.1|DC905153
EST:     TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACG                         CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
genomic: TATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG

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: 15

GTTGAAGATTTTGAGTTGGTGAAAGTATACTTAAAAGCTGGAGAGCACGACGCTCCATCATGGACCTCCATGACGgtgaagaatc ... tgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtacgttcgcaatgactgaaatctaacttggaaaactggactgtgatgcagCCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG
                        atctaac  putative branch site (score: 15)
                      aaatctaa  TA-rich tract