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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttatctggatccacttctactcctcacttcattaccttattcgttcttgttttccccttaaatcccccccatttagatgtataaggttgcgcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGCAGTTCCGTTGTGGACGTGCCCCTGGATTACCTTGTCATGGGATGCCGAG

Basic information

species Physcomitrella patens
transcript PP1S62_204V6.1
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|162247294|gb|FC421415.1|FC421415
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
EST: gi|67692818|gb|BJ953051.1|BJ953051
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
EST: gi|15261345|gb|BI436655.1|BI436655
EST:     TTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         A-TGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
genomic: TTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
EST: gi|162218004|gb|FC393688.1|FC393688
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTTTGC
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
EST: gi|162247295|gb|FC421416.1|FC421416
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
EST: gi|67569550|gb|BJ942374.1|BJ942374
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTA
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTA
EST: gi|162218005|gb|FC393689.1|FC393689
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
EST: gi|162237708|gb|FC413323.1|FC413323
EST:     CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAG                         ATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC
genomic: CGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGC

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), 35 (downstream exon)
Score: 11

TCCTTTGCAAGAAGCAGAAAACATAATTTACCAGCAGAATTACCAATTGACGATTGACGAAGAACTTAAGACGGTTCTACATGAAGCTGTAGCGAAGAAGgtaagcttta ... gcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGCAGTTCCGTTGTGGACGTGCCCCTGGATTACCTTGTCATGGGATGCCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttttccccttaaatcccccccatttagatgtataaggttgcgcgagtgcagATTGTCGTGGTCTTCAAGGTCTACTGGGGCGACGCTAAGGAGAAGCTCTGCAGTTCCGTTGTGGACGTGCCCCTGGATTACCTTGTCATGGGATGCCGAG
                         atttagatgtataa  TA-rich tract