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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgttcgttcagctggcatttaatgcattgtttggctttccatgcggttagattcggtccacgctctgattctaatctttcatggtcgcttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG

Basic information

species Physcomitrella patens
transcript PP1S103_13V6.1
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|100422270|gb|BY957941.1|BY957941
EST:     TGATAGGGGTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCG                         ACGGGTAGCTTTGCTGAGGACATGATACCCACG
genomic: TGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCGgttcgtgcct ... ttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG
EST: gi|100354463|gb|BY983432.1|BY983432
EST:     TGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCG                         ACGGGTAGCTTTGCTGAGGACATGATACCCACG
genomic: TGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCGgttcgtgcct ... ttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG
EST: gi|100383532|gb|BY950316.1|BY950316
EST:     TGATAGGGTTGCAAA-TGCTGGCAAAACTTCTCTCGTGAATGTCATTGCG                         ACGGGTAGCTTTGCTGAGGACATGATACCCACG
genomic: TGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCGgttcgtgcct ... ttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG
EST: gi|100422708|gb|BY957961.1|BY957961
EST:     TGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCG                         ACGGGTAGCTTTGCTGAGGACATGATACCCACG
genomic: TGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCGgttcgtgcct ... ttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG

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: 35 (upstream exon), 35 (downstream exon)
Score: 24

CCTATTTTTCAAGCAAGAGATGGAGTTGTCTTTGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCGgttcgtgcct ... ttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttagattcggtccacgctctgattctaatctttcatggtcgcttctgtgcagACGGGTAGCTTTGCTGAGGACATGATACCCACG
                         ttctaat  putative branch site (score: 24)
                                         tcgcttct  putative PPT
                        attctaat  TA-rich tract