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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgaattgactcatctgtcattttcgatgcattcgttccattgactcaatactcagcttcggtgccctcttggagttctgaggatgttccgttgttttgggtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG

Basic information

species Physcomitrella patens
transcript PP1S9_234V6.1
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|162183943|gb|FC360249.1|FC360249
EST:     TGATGAACGTGAAAGACCTTACCCTGGCTCATGTGAAGAGCCACTTACAG                         ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
genomic: TGATGAACGTGAAAGACCTTACCCTGGCTCATGTGAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
EST: gi|37823355|gb|BJ581421.1|BJ581421
EST:     CCCTGGCTCATGTGAAGAGCCACTTACAG                         ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
genomic: CCCTGGCTCATGTGAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
EST: gi|18341786|gb|BJ173821.1|BJ173821
EST:     GCTCATGTGAAGAGCCACTTACAG                         ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
genomic: GCTCATGTGAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
EST: gi|162255475|gb|FC431889.1|FC431889
EST:     TGATGAACGTGAAAGACCTTACCCTGGCTCATGTGAAGAGCCACTTACAG                         ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
genomic: TGATGAACGTGAAAGACCTTACCCTGGCTCATGTGAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
EST: gi|37828323|gb|BJ586335.1|BJ586335
EST:     GGCTCATGTGAAGAGCCACTTACAG                         ATGTATCGGACTGTGAAAACTTCCGACAAGGTCAGGTCGTTCTCCAG
genomic: GGCTCATGTGAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAA-GTCAGGTCGTTCTCCAG
EST: gi|18336785|gb|BJ168808.1|BJ168808
EST:     GAAGAGCCACTTACAG                         ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
genomic: GAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG

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: 27 (upstream exon), 35 (downstream exon)
Score: 27

GAGCAACACCGAAATCTGTTCTGGAGCTGATGAACGTGAAAGACCTTACCCTGGCTCATGTGAAGAGCCACTTACAGgtctgtgaat ... gtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcggtgccctcttggagttctgaggatgttccgttgttttgggtgagtgcagATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG
                                    ttgtttt  TA-rich tract