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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggggcttgaaacacttaatctccaataatcggatttttttttaccttggtattggtattgcacttttggagtagcaccaaattagacagaaatttgagtaggcgatgaatcctcgaaattgtttagcacacacctttgtctagtgcacagtagttaatgctccagagtttcaagcatttttaatggtacttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGCATGATATTGATCGTACTCACCTATCCCGACTTATG

Basic information

species Physcomitrella patens
transcript PP1S86_24V6.1
intron # 11
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|162166443|gb|FC342425.1|FC342425
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|19788036|gb|BQ040704.1|BQ040704
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|18339175|gb|BJ171202.1|BJ171202
EST:     GGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: GGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|37822050|gb|BJ580116.1|BJ580116
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|37840029|gb|BJ598037.1|BJ598037
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|162164168|gb|FC339591.1|FC339591
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|162164169|gb|FC339592.1|FC339592
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|37844633|gb|BJ602641.1|BJ602641
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|37828890|gb|BJ586902.1|BJ586902
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|37825014|gb|BJ583080.1|BJ583080
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
EST: gi|37829827|gb|BJ587839.1|BJ587839
EST:     CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCG                         GATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC
genomic: CAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGC

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: 29 (upstream exon), 35 (downstream exon)
Score: 6

CATTCAAGCTATCCTTCATTTGGGCTAGGCAATCAATTCGCTTTTAAGCTCAAGGTGACGGGTCGCGATGGAACGGAGCAAAACCATCGCTTCAACTGCGgtggggcttg ... acttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGCATGATATTGATCGTACTCACCTATCCCGACTTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcacagtagttaatgctccagagtttcaagcatttttaatggtacttttgcagGATCTGAGAGCTTGACTGAGCTTATGTCCATGATAGCCCAGCGTGTTGGGCATGATATTGATCGTACTCACCTATCCCGACTTATG
                                   ttttaat  putative branch site (score: 6)
                                            tactttt  putative PPT
                                 atttttaat  TA-rich tract