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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATTGGCACAAATCTTATAGCCGCTCCCGTCCCAGCTGCGCGATCTTCTGGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgtgtttcgttcactttcaagcggtttgcttgtttgtctacctagggattcagacaaaattcgtttgttcttatcatatagagcggtcgttaaataaggattttatgtgctgcataactttctagccacttatgaagcatggtgtttttgtag

Basic information

species Physcomitrella patens
transcript PP1S4_67V6.1
intron # 5
splice site 5'
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|208371454|gb|DC955790.1|DC955790
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|162275225|gb|FC451201.1|FC451201
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|67693139|gb|BJ953372.1|BJ953372
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|208386074|gb|DC956590.1|DC956590
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|67727816|gb|BJ978075.1|BJ978075
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|37824585|gb|BJ582651.1|BJ582651
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|208380155|gb|DC927434.1|DC927434
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG
EST: gi|208373986|gb|DC944719.1|DC944719
EST:     GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATC                         TATGCCTTTTACTCGAGGACCTGGGTCTGATCGAGGCAGAAGTGGTAGCAG
genomic: GGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 16

TGATTGGCACAAATCTTATAGCCGCTCCCGTCCCAGCTGCGCGATCTTCTGGAGCCATGGCAATGGTTGCTAGTCGAGGACGTCCTGTTTCTTCGTCATCgtaagtttgt ... gtttttgtagTATGCCTTTTACTCGAGGACCTGGATCTGATCGAGGCAGAGGTGGTAGCAGCGCATTTCGGGGACGTGGCGGTGGCAGAAGTGCTGGCGGTGCAGGTGCT




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