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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaaatttgatgaaattctgctgttggctgatttggtttatctcgaggatgaaaacgtgaatcgtgccgttctaattagccctagcttcactgggtgttgaatattgaatttcgttgcatatgttaacttgtgtgccgattttgtttgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGGTACTCTAAACTTGCGGCAGTAGTTCTAGTTAGTTTGCCTCCACCACCCC

Basic information

species Physcomitrella patens
transcript PP1S14_51V6.1
intron # 15
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|162176265|gb|FC352722.1|FC352722
EST:     GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAN                         GTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
genomic: GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
EST: gi|162238870|gb|FC417673.1|FC417673
EST:     GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAG                         GTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
genomic: GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
EST: gi|162238869|gb|FC417672.1|FC417672
EST:     GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAG                         GTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
genomic: GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
EST: gi|162160118|gb|FC335988.1|FC335988
EST:     GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAG                         GTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
genomic: GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
EST: gi|37847937|gb|BJ605945.1|BJ605945
EST:     GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAG                         GTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
genomic: GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
EST: gi|18341010|gb|BJ173042.1|BJ173042
EST:     GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAG                         GTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG
genomic: GTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGG

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), 29 (downstream exon)
Score: 6

AAAAGCTCGCAAGCGGATCACAGTCCGTGTGGAGGAAATGAAGCAAGTCTGTGGTGATAGCAAGTTTGAGGCGGATTATAGTCCTTTCAACGAGCACCAGgtgagcaaat ... tgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGGTACTCTAAACTTGCGGCAGTAGTTCTAGTTAGTTTGCCTCCACCACCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgaatttcgttgcatatgttaacttgtgtgccgattttgtttgtacttcagGTGAACAAGTTTTTGTATACAACATTAAAGCTCAATTCTATCATTTTACGGTACTCTAAACTTGCGGCAGTAGTTCTAGTTAGTTTGCCTCCACCACCCC
                    tgttaac  putative branch site (score: 6)
                                      ttttgttt  putative PPT
                 atatgttaa  TA-rich tract