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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaacacttcaattgtcatggattcggtggatttgttttagaggttgatggtttgtgtcggaacagaagtaactttgattggtttctgttttagtggtctcggcattcgtagaagagatcccacattcaatgtctaagctgtgcag

Basic information

species Physcomitrella patens
transcript PP1S69_234V6.1
intron # 2
splice site 5'
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|208375174|gb|DC945324.1|DC945324
EST:     ACTTGCNATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|208369164|gb|DC956039.1|DC956039
EST:     AC-TGCNATCAAAGTATGACGT-GNTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|208387415|gb|DC949200.1|DC949200
EST:     AC-TGCNATC-AAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|162241075|gb|FC417733.1|FC417733
EST:     TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|67697171|gb|BJ957404.1|BJ957404
EST:     ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGANTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|208388297|gb|DC949297.1|DC949297
EST:     ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: ACTTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|208363965|gb|DC947209.1|DC947209
EST:     NTGCNATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|208352536|gb|DC918245.1|DC918245
EST:     C-TGCNATCAAAGTATGACGTGGTTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: CTTGCAATCAAAGTATGACGTGG-TTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|162179728|gb|FC356319.1|FC356319
EST:     ATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: ATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|162226950|gb|FC403333.1|FC403333
EST:     TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|162204327|gb|FC380515.1|FC380515
EST:     TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|37840597|gb|BJ598605.1|BJ598605
EST:     TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
EST: gi|162226951|gb|FC403334.1|FC403334
EST:     TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAG                         TTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC
genomic: TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCAC

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), 34 (downstream exon)
Score: 24

TTGCAATCAAAGTATGACGTGGTTCGATGAGACCGCGGGTGACTTCAGgtacacaaca ... agctgtgcagTTATATCGACACGAAGAGCGTGTCCGGAGGGAACGGAGAATGCAGTGCCACAAACGGTTGGTCCTTTGGAACCTGCGGTGATGATGATTCAAGCGAATGC




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