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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgcgtccgctttgtctgcgtatattgcaacagagacgtggagaatcggatgatattatcccatctaactgggttgtctgttgttgtacttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAAGCCTCAGGCCCTCCAGAGCCTATCCCTGTTACTGCCATAGCGTCAAAGT

Basic information

species Physcomitrella patens
transcript PP1S47_50V6.1
intron # 5
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|37831034|gb|BJ589046.1|BJ589046
EST:     GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|162161503|gb|FC338710.1|FC338710
EST:     GTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: GTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|208398717|gb|DC916240.1|DC916240
EST:     GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|162161504|gb|FC338711.1|FC338711
EST:     GAGTGGGTGTCCCCGNTGTATACGACTCGGTCGGCAAAGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTT
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTT
EST: gi|208357885|gb|DC902367.1|DC902367
EST:     GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCA
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCA
EST: gi|100357893|gb|BY946627.1|BY946627
EST:     GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACCTTTCAA                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGT
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGT
EST: gi|162273277|gb|FC449557.1|FC449557
EST:     GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|208368855|gb|DC947413.1|DC947413
EST:     GTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: GTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|100434852|gb|BY960844.1|BY960844
EST:     GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: GAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|37830854|gb|BJ588866.1|BJ588866
EST:     TGTATACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: TGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
EST: gi|37825621|gb|BJ583687.1|BJ583687
EST:     ACGACTCGGTCGGCAAGGATACGTTTCAG                         GCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA
genomic: ACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAA

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: 34 (upstream exon), 24 (downstream exon)
Score: 10

TGTGTACTCCGACAATAATCTTGTGGAGAGAGTGAAGGAAATTACAAAAGGAGTGGGTGTCCCCGTTGTATACGACTCGGTCGGCAAGGATACGTTTCAGgtttagcacc ... acttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAAGCCTCAGGCCCTCCAGAGCCTATCCCTGTTACTGCCATAGCGTCAAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcggatgatattatcccatctaactgggttgtctgttgttgtacttgtacagGCATCGTTGGAATGCTTGGCTTACCGAGGAATGCTTGTTTTGTACGGGCAAGCCTCAGGCCCTCCAGAGCCTATCCCTGTTACTGCCATAGCGTCAAAGT
                    atctaac  putative branch site (score: 10)
       atgatattat  TA-rich tract