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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatatgtagcatgcctaattgttttcattctattctctcatgttatcagagatgaatagtagccacgttaattggagtgagtgtccattgtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGAAAATAGCTTCAATATGTATGCCCGAGCGGCTCAACAAATTTATGCTCCC

Basic information

species Physcomitrella patens
transcript PP1S99_220V6.1
intron # 2
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|18361408|gb|BJ193474.1|BJ193474
EST:     GNNNNNNNNNCGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATG                         AGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
genomic: GAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
EST: gi|18367261|gb|BJ199343.1|BJ199343
EST:     GNNNNNNNNNCGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATG                         AGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
genomic: GAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
EST: gi|18372621|gb|BJ204223.1|BJ204223
EST:     GNNNNNNNNNCGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATG                         AGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
genomic: GAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
EST: gi|18362975|gb|BJ195047.1|BJ195047
EST:     GNNNNNNNNNCGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATG                         AGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
genomic: GAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
EST: gi|162165453|gb|FC342020.1|FC342020
EST:     GNNNNNNNNNCGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATG                         AGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
genomic: GAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
EST: gi|162158052|gb|FC334453.1|FC334453
EST:     GNNNNNNNNNCGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATG                         AGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA
genomic: GAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGA

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: 31 (upstream exon), 34 (downstream exon)
Score: 15

CAACTGAAGAAAAAAAAACGGAAGCAGTTGTTACACACTCTGGGAAAAATCAAGGATGgcaagtaact ... gtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGAAAATAGCTTCAATATGTATGCCCGAGCGGCTCAACAAATTTATGCTCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagagatgaatagtagccacgttaattggagtgagtgtccattgtgtgttcagAGCTCATGCTTCTGGGGTTCATATCCCTTTCCCTCACCGTCTTCCAGTCGAAAATAGCTTCAATATGTATGCCCGAGCGGCTCAACAAATTTATGCTCCC
                     cgttaat  putative branch site (score: 15)
                       ttaatt  TA-rich tract