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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaagaattcatcattcgcaatgtgtacaatgtcttgatgatgataatgaattgtccaattctacattgcttacgataatttgtcgctgtcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCATGGGCGAAACCGACCTTG

Basic information

species Physcomitrella patens
transcript PP1S425_16V6.1
intron # 2
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|208348546|gb|DC905825.1|DC905825
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCC
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCC
EST: gi|208384789|gb|DC907402.1|DC907402
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
EST: gi|100358086|gb|BY965465.1|BY965465
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTT
EST: gi|162186160|gb|FC361364.1|FC361364
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
EST: gi|100442509|gb|BY963203.1|BY963203
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAGCCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
EST: gi|18355551|gb|BJ187610.1|BJ187610
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
EST: gi|18350239|gb|BJ182290.1|BJ182290
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
EST: gi|162265882|gb|FC442885.1|FC442885
EST:     AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCG                         GAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT
genomic: AGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCAT

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), 34 (downstream exon)
Score: 13

AGAACAGTCAGGCGTGTCTCATAGCATTACACACAGGAGCGTTTTAGAGGTTTCGTCGGTGAACATCCTGGGCGCCACAGCATTTGAAACCTCCGgtaagtcctt ... tcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCATGGGCGAAACCGACCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgaattgtccaattctacattgcttacgataatttgtcgctgtcttgagcagGAACCCCTGCTGATTGTGTCTCGTTGGCATTGACATCGTCTATTTTCCCATGGGCGAAACCGACCTTG
                       tgcttac  putative branch site (score: 13)
                                          ctgtctt  putative PPT
                               ataatttgt  TA-rich tract