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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtgcaaaatacaacctttgactacatgattgctaactcgataaacacgcatttattcctactaacattgaactcaccgcattttgattcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGGAATACATTCCAAGCCAATCCCAAAGGCCAAAAGTCATCCAAGAGTGCCG

Basic information

species Physcomitrella patens
transcript PP1S140_172V6.1
intron # 3
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|208350886|gb|DC909933.1|DC909933
EST:     CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAG                         CGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
genomic: CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAGgttttcgcat ... tcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
EST: gi|100360499|gb|BY983815.1|BY983815
EST:     CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAG                         CGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
genomic: CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAGgttttcgcat ... tcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
EST: gi|208357242|gb|DC910653.1|DC910653
EST:     CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAG                         CGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
genomic: CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAGgttttcgcat ... tcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
EST: gi|208358940|gb|DC939224.1|DC939224
EST:     CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAG                         CGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
genomic: CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAGgttttcgcat ... tcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
EST: gi|162252651|gb|FC428688.1|FC428688
EST:     CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAG                         CGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG
genomic: CAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAGgttttcgcat ... tcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGG

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: 24 (upstream exon), 26 (downstream exon)
Score: 6

TGTGAGATGACAGGTCATCCAGAGATACCAGTTGCGGAAGGACCCTCTGAACCGTTGAAGgttttcgcat ... tcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGGAATACATTCCAAGCCAATCCCAAAGGCCAAAAGTCATCCAAGAGTGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacgcatttattcctactaacattgaactcaccgcattttgattcttgaacagCGGGTCAAACCTCGAATTGCGTATTTTGTGCATGGTTCGGATGGCCTTGGGAATACATTCCAAGCCAATCCCAAAGGCCAAAAGTCATCCAAGAGTGCCG
                                            ttctt  CT-rich tract
                                     attttgatt  TA-rich tract