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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatatttgtcaggcaaagttactatttggaagtgtcttaactagaatttgtcaaattttgtttgcttgttaattaagttcagtgggtggatgatgtagTGTGAAACACGAGTATGAAGCTTGGGAAGGCGAGAAGACCAAGTTGAAGTCCTGCAACCCATCCGAAGCAGCGACTCGTCAACCTCCCCAGGAAGTTGTT

Basic information

species Physcomitrella patens
transcript PP1S24_182V6.1
intron # 5
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|162256884|gb|FC432986.1|FC432986
EST:     CCTGTTTCCACAGCTTCTCGAATTGTTGGCTTTGAAGTGGCTCCTCAGAG                         TGTGAAACACGAGTATGAAGCTTGGGAAGGCGAGAAGACCAAGTTGAAGTC
genomic: CCTGTTTCCACAGCTTCTCGAATTGTTGGCTTTGAAGTGGCTCCTCAGAGgtctgtcatc ... gatgatgtagTGTGAAACACGAGTATGAAGCTTGGGAAGGCGAGAAGACCAAGTTGAAGTC
EST: gi|100405258|gb|BY955435.1|BY955435
EST:     CCTGTTTCCACAGCTTCTCGGATTGTTGGCTTTGAAGTGGCTCCTCAGAG                         TGTGAAACACGAGTATGAAGCTTGGGAAGGCGA
genomic: CCTGTTTCCACAGCTTCTCGAATTGTTGGCTTTGAAGTGGCTCCTCAGAGgtctgtcatc ... gatgatgtagTGTGAAACACGAGTATGAAGCTTGGGAAGGCGA

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: 32 (upstream exon), 25 (downstream exon)
Score: 5

AATATTTCATCTTTAACCACCTCAGCTTCGTAGTGTATTATCATCAAGATCCTGTTTCCACAGCTTCTCGAATTGTTGGCTTTGAAGTGGCTCCTCAGAGgtctgtcatc ... gatgatgtagTGTGAAACACGAGTATGAAGCTTGGGAAGGCGAGAAGACCAAGTTGAAGTCCTGCAACCCATCCGAAGCAGCGACTCGTCAACCTCCCCAGGAAGTTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttgtcaaattttgtttgcttgttaattaagttcagtgggtggatgatgtagTGTGAAACACGAGTATGAAGCTTGGGAAGGCGAGAAGACCAAGTTGAAGTCCTGCAACCCATCCGAAGCAGCGACTCGTCAACCTCCCCAGGAAGTTGTT
                       tgttaat  putative branch site (score: 5)
                      ttgttaattaagtt  TA-rich tract