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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGCTTTCGAAGATTTGTCAGGACATACTGACGATCATCGACGAGCACTTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatgtcctgagcggatgaagtggggagtgattgggaaggaatgtgtggtgtactttgcgtgttattgcaatgtgcaccgtggaggcgcagtacc...

Basic information

species Physcomitrella patens
transcript PP1S348_9V6.1
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|18331317|gb|BJ163327.1|BJ163327
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGA
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGA
EST: gi|208389853|gb|DC937684.1|DC937684
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208395820|gb|DC911857.1|DC911857
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|18350889|gb|BJ182940.1|BJ182940
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|18359345|gb|BJ191406.1|BJ191406
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCCGGAGTTCAAGACCGGGAATGAGA
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGC-GGAGTTCAAGACCGGGAATGAGA
EST: gi|18375345|gb|BJ206923.1|BJ206923
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67717893|gb|BJ968152.1|BJ968152
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67704802|gb|BJ965035.1|BJ965035
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67508215|gb|BJ941086.1|BJ941086
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208361629|gb|DC942858.1|DC942858
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162249894|gb|FC425695.1|FC425695
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208377815|gb|DC940927.1|DC940927
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67717603|gb|BJ967862.1|BJ967862
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|100444344|gb|BY982373.1|BY982373
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG

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), 32 (downstream exon)
Score: 17

AAGAGCTTTCGAAGATTTGTCAGGACATACTGACGATCATCGACGAGCACTTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG




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