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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCTGCAGTAGAGACTTGATACTTCCTCCCTTCAAACCCACTTTCGTGTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAGgtgcgaggctgatgatgcctgtattggaccaatacctttcgtgcctgttttcgaactgctttggtttgtattcgcgccttttctttttcttttttttttt...

Basic information

species Physcomitrella patens
transcript PP1S6_239V6.1
intron # 1
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|100386406|gb|BY951202.1|BY951202
EST:     GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAG                         GTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG
genomic: GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAGgtgcgaggct ... ttgggggcagGTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG
EST: gi|18369014|gb|BJ201099.1|BJ201099
EST:     GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAN                         GTGGTTGCTATGGGTGACGCGGCGCANGTTCGGATGCCAGAAGGACAATGG
genomic: GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAGgtgcgaggct ... ttgggggcagGTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG
EST: gi|100386366|gb|BY988033.1|BY988033
EST:     GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAG                         GTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG
genomic: GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAGgtgcgaggct ... ttgggggcagGTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG
EST: gi|100368622|gb|BY967097.1|BY967097
EST:     GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAG                         GTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG
genomic: GTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAGgtgcgaggct ... ttgggggcagGTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGG

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), 32 (downstream exon)
Score: 4

TGATGCTGCAGTAGAGACTTGATACTTCCTCCCTTCAAACCCACTTTCGTGTTTTGAGGTTCCTCGGCGGCTTTGGGTTTCATTTTTCCATTGCGACCAGgtgcgaggct ... ttgggggcagGTGGTTGCTATGGGTGGCGCGGCGCAGGTTCGGATGCCAGAAGGACAATGGGATTGGCGGCAGATGGCTGCAGTGAAGATGTCAACGGAATACGACTCCG




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