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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAACTGGAGTTTACAAACATCTTTTCGGTGGCTTCATGGGAGGGCACGCTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaatttatttgttattttacacaagtgttgagctgatgcgctattggcgattatcattgaataatttctggattagattgactgggatcgttgtttgactgatattttgtccatgcag

Basic information

species Physcomitrella patens
transcript PP1S7_406V6.1
intron # 9
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|208350585|gb|DC922114.1|DC922114
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162154869|gb|FC331911.1|FC331911
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162162643|gb|FC338945.1|FC338945
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|37847527|gb|BJ605535.1|BJ605535
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162250069|gb|FC427378.1|FC427378
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|208376893|gb|DC918792.1|DC918792
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162250070|gb|FC427379.1|FC427379
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|37850322|gb|BJ608330.1|BJ608330
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|208398626|gb|DC920521.1|DC920521
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162161580|gb|FC338787.1|FC338787
EST:     GTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         CCCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: GTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162195749|gb|FC371140.1|FC371140
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGNGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162195748|gb|FC371139.1|FC371139
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|162171828|gb|FC348978.1|FC348978
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|208345947|gb|DC921104.1|DC921104
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
EST: gi|19789964|gb|BQ041614.1|BQ041614
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGG
EST: gi|37843562|gb|BJ601570.1|BJ601570
EST:     CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGG                         ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG
genomic: CTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG

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: 31 (upstream exon), 34 (downstream exon)
Score: 14

CAAAACTGGAGTTTACAAACATCTTTTCGGTGGCTTCATGGGAGGGCACGCTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaa ... gtccatgcagACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAACTGGAGTTTACAAACATCTTTTCGGTGGCTTCATGGGAGGGCACGCTGTGAAGCTTATTGGATGGGGAACCACCGACGATGGTGTGGACTACTGGgtacgtggaatttatttgttattttacacaagtgttgagctgatgcgctattggcgattatcattgaataatttctggattagattgactgggatcgttgtttgactgatattttgtccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC