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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGATGTTGTCTTTTTTGTCGGTGGATCTGTATGGACGTTGGACTGGTGTCCTCGTAGACCCGGATGGTCGTCTCAGGTCATTCAGAATGAGgtgctgatttttgaggcgtactgtattcagcacctacatcttgtttcttcgcctcgttctgatgcgatatttgtcatcacatttaacttttatgtccagttgtcaggaacgtcgtaagctgaaaatacgtgtggtccattctcag

Basic information

species Physcomitrella patens
transcript PP1S397_28V6.2
intron # 4
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|208358461|gb|DC930593.1|DC930593
EST:     ACTGGTGTCCTCGTAGACCCGGATGGTCGTCTCANGTCATTCAGAATGAG                         TTTCTTGTGGTAGGAGCACACCCAAGACAATCGCCACATCATAGGCTCGGC
genomic: ACTGGTGTCCTCGTAGACCCGGATGGTCGTCTCAGGTCATTCAGAATGAGgtgctgattt ... ccattctcagTTTCTTGTGGTAGGAGCACACCCAAGACAATCGCCACATCATAGGCTCGGC
EST: gi|18325655|gb|BJ157652.1|BJ157652
EST:     ACTGGTGTCCTCGTAGACCCGGATGGTCGTCTCAGGTCATTCAGAATGAG                         TTTCTTGTGGTAGGAGCACACCCAAGAC
genomic: ACTGGTGTCCTCGTAGACCCGGATGGTCGTCTCAGGTCATTCAGAATGAGgtgctgattt ... ccattctcagTTTCTTGTGGTAGGAGCACACCCAAGAC

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), 33 (downstream exon)
Score: 2

CGCGGATGTTGTCTTTTTTGTCGGTGGATCTGTATGGACGTTGGACTGGTGTCCTCGTAGACCCGGATGGTCGTCTCAGGTCATTCAGAATGAGgtgctgattt ... ccattctcagTTTCTTGTGGTAGGAGCACACCCAAGACAATCGCCACATCATAGGCTCGGCGAATCATTGCATGGGAAAGGTTTGTTGCAAATATGGGCAATTGATCTCA




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