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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcattttatatttatttcaaaagaatcgctcatgatttcagttctcgattctagcagtgcaacagattcaagttcatgaaggaatagaaacgatttagggttgataatgtttttagggtcaactttttcatgaaattttctcttcggctacaacaatgctctgacggttgcgtcttttttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACCTTCATGTTCAGCAATTTTGTGGCTAGCCGGGTCCAGTTCACCTTTTATT

Basic information

species Physcomitrella patens
transcript PP1S134_26V6.1
intron # 7
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|162235645|gb|FC411390.1|FC411390
EST:     GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAG                         GATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
genomic: GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAGgtagcatttt ... ttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
EST: gi|162189954|gb|FC365618.1|FC365618
EST:     GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAG                         GATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
genomic: GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAGgtagcatttt ... ttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
EST: gi|37843892|gb|BJ601900.1|BJ601900
EST:     GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAG                         GATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
genomic: GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAGgtagcatttt ... ttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
EST: gi|37831023|gb|BJ589035.1|BJ589035
EST:     GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAG                         GATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
genomic: GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAGgtagcatttt ... ttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
EST: gi|37845078|gb|BJ603086.1|BJ603086
EST:     GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAG                         GATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC
genomic: GTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAGgtagcatttt ... ttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACC

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: 33 (upstream exon), 14 (downstream exon)
Score: 3

ACTCCCTGGAGTCAATGCTTCAGAAAACCGTATTATGGACTCCAGCGTTAGTCATTCGTCAAGTTCAAAGCAATCTGAAGGGACTAGTGCAATGGAAGAGgtagcatttt ... ttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACCTTCATGTTCAGCAATTTTGTGGCTAGCCGGGTCCAGTTCACCTTTTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttctcttcggctacaacaatgctctgacggttgcgtcttttttctaagcagGATTAAGTACGAAGGAGGTTCTTATAGCTGTCTATGTATCTGCATTGGACCTTCATGTTCAGCAATTTTGTGGCTAGCCGGGTCCAGTTCACCTTTTATT
                         ctctgac  putative branch site (score: 3)
                                  ttgcgtcttttttct  putative PPT
                                         ttttttctaa  TA-rich tract