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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggaatgttcatttcgctgtcaacagatcttttataggtactctagactaaagggacgcgatttgttacgttctgatacgatacgagttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTTTTCTTCTTGAGAATGGTGCTTTTCTTGCGCCGGACATGACTGATGGTCG

Basic information

species Physcomitrella patens
transcript PP1S77_25V6.2
intron # 5
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|162186890|gb|FC363134.1|FC363134
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
EST: gi|37835619|gb|BJ593631.1|BJ593631
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
EST: gi|162167138|gb|FC343614.1|FC343614
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
EST: gi|37828694|gb|BJ586706.1|BJ586706
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
EST: gi|37831487|gb|BJ589499.1|BJ589499
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
EST: gi|162154471|gb|FC330473.1|FC330473
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
EST: gi|162159379|gb|FC335167.1|FC335167
EST:     TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGAT                         GGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT
genomic: TTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTT

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), 35 (downstream exon)
Score: 48

GCTCTTCACCTTGCTGCTGCTGGTGGGCATATTGATGTGATGGATGAGCTTTTGGAGCGTGGTGCGGATATTGATGTTCGTACGAAAGGTGGTTGTGGATgtgagtgcgc ... ttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTTTTCTTCTTGAGAATGGTGCTTTTCTTGCGCCGGACATGACTGATGGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagactaaagggacgcgatttgttacgttctgatacgatacgagttatctgcagGGACTCCTCTTCACAACGCTGCCAAAGAGAGAAATAGAAAAGCAGTTCGTTTTCTTCTTGAGAATGGTGCTTTTCTTGCGCCGGACATGACTGATGGTCG
                  atttgtta  TA-rich tract