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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctcatgccttgctggtgcctgtttccattcgtccagtgtacggagcaccgattgtactgtggcgttgtgaagctggatggggagattcgaggt...

Basic information

species Physcomitrella patens
transcript PP1S167_1V6.1
intron # 7
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|67727151|gb|BJ977410.1|BJ977410
EST:     ATGGTCTCGGCGAGTTNGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAA
genomic: ATGGTCTCGGCGAGTT-GCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAA
EST: gi|162260908|gb|FC437965.1|FC437965
EST:     CGAGTAGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: CGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162239319|gb|FC415405.1|FC415405
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGGACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|67695406|gb|BJ955639.1|BJ955639
EST:     CGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTGAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: CGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162183902|gb|FC360208.1|FC360208
EST:     GCGAGTTGCCGCAG                         GGGTTCGCCCGTCTGAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|100420810|gb|BY993515.1|BY993515
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGGTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162249711|gb|FC426825.1|FC426825
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162167541|gb|FC343712.1|FC343712
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|67726787|gb|BJ977046.1|BJ977046
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162194880|gb|FC368997.1|FC368997
EST:     CGAGTTGCCGCAG                         GGGTTCGCCCGTCTGAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: CGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162239318|gb|FC415404.1|FC415404
EST:     GCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162179697|gb|FC355755.1|FC355755
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|100410627|gb|BY992191.1|BY992191
EST:     NNNNNTCGCCGTACATCTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGC
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGC
EST: gi|67700068|gb|BJ960301.1|BJ960301
EST:     CGGCGAGTTGCCGCAG                         GGGTTCGCCCGTNTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: CGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|208370153|gb|DC951752.1|DC951752
EST:     GGGGGTCGCCGTACA-TTACCCGCTGTATNGTCTCGGCGAGTTGCTGCAG                         GGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
EST: gi|162194881|gb|FC368998.1|FC368998
EST:     NNNNNTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG                         GGGTTCGCCCGTCTGAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA
genomic: GGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAA

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), 31 (downstream exon)
Score: 19

TTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAGgtatgtcctc ... tttgttgcagGGGTTCGCCCGTCTAAGTGCAGTGTACGGAGGAACTTACATGCTTGCCAAACCGGAGTGCAAG




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