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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaggaggttccaaaccttaactttgaagcattaagctttatatcctctctcctctttggtaatatatgcagtttgcgaatttgtaggcgtaatgctttcatgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG

Basic information

species Physcomitrella patens
transcript PP1S113_31V6.1
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|67709650|gb|BJ965466.1|BJ965466
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGG
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
EST: gi|208370860|gb|DC936898.1|DC936898
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
EST: gi|67717411|gb|BJ967670.1|BJ967670
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
EST: gi|162235503|gb|FC411833.1|FC411833
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
EST: gi|208378113|gb|DC902586.1|DC902586
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
EST: gi|18374186|gb|BJ205764.1|BJ205764
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAAATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGG
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGG
EST: gi|100415055|gb|BY975143.1|BY975143
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGGTTCTTGA
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
EST: gi|162151133|gb|FC327652.1|FC327652
EST:     CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATG                         GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA
genomic: CTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGA

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), 10 (downstream exon)
Score: 2

CTTGCGTGCTACTTCCATCGAAGATACAAATCAAGCAAGTCGAGCACCTACAAGGAAGATGgtatggagga ... tgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtaatatatgcagtttgcgaatttgtaggcgtaatgctttcatgttttgtagGAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG
                                       ctttcat  CT-rich tract
     aatatat  TA-rich tract