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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaattttagaagcttcttgtatttcttgttcttgttagcgaagtaagattccacattgccacaggcttctgtctcatgattgacctttctatgtgcagTGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCAGAAATTGTGTTCAACTCTAGAGCCGCTTCTTCGGAAAATG

Basic information

species Physcomitrella patens
transcript PP1S51_322V6.1
intron # 1
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|18352994|gb|BJ185049.1|BJ185049
EST:     TCCAAGGATGGTATGCCGGAAGAAAAGCGGCCGCGCCCACAGCTTGCCAG                         TGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCACAAATTGTGTTCAAC
genomic: TCCAAGGATGGTATGCCGGAAGAAAAGCGGCCGCGCCCACAGCTTGCCAGgtttggacac ... ctatgtgcagTGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCAGAAATTGTGTTCAAC
EST: gi|18330740|gb|BJ162746.1|BJ162746
EST:     TCCAAGGATGGTATGCCGGAAGAAAAGCGGCCGCGCCCACAGCTTGCCAG                         TGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCAGAAATTGTGTTCAAC
genomic: TCCAAGGATGGTATGCCGGAAGAAAAGCGGCCGCGCCCACAGCTTGCCAGgtttggacac ... ctatgtgcagTGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCAGAAATTGTGTTCAAC

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: 26 (upstream exon), 30 (downstream exon)
Score: 10

GCTCAAGTATTGGTGTCGGAATGTCGAGAGAGAAGCGTGAAAGAGATGGCTCCAAGGATGGTATGCCGGAAGAAAAGCGGCCGCGCCCACAGCTTGCCAGgtttggacac ... ctatgtgcagTGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCAGAAATTGTGTTCAACTCTAGAGCCGCTTCTTCGGAAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagattccacattgccacaggcttctgtctcatgattgacctttctatgtgcagTGTCATTGTTGAAGCTGTGAAAATGGACTGTATGCAGAAATTGTGTTCAACTCTAGAGCCGCTTCTTCGGAAAATG
                                  gattgac  putative branch site (score: 10)
                                        cctttctat  CT-rich tract
                                          tttctat  TA-rich tract