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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttaaaatttgttttgacataagtttatggggatttgtcaattttcagctcaaaaattatagtcttaacatctcttcattgggtgtaaaattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTTATCAAATCTGTGAGGGATCTTTCTAGGGATGTTATTAAG

Basic information

species Physcomitrella patens
transcript PP1S83_162V6.1
intron # 11
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|37852112|gb|BJ610120.1|BJ610120
EST:     TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
EST: gi|208383459|gb|DC923611.1|DC923611
EST:     TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
EST: gi|162167398|gb|FC343101.1|FC343101
EST:     TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
EST: gi|162177829|gb|FC355079.1|FC355079
EST:     TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
EST: gi|37836032|gb|BJ594040.1|BJ594040
EST:     TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
EST: gi|162240587|gb|FC419364.1|FC419364
EST:     TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAATCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
EST: gi|37835488|gb|BJ593500.1|BJ593500
EST:     TCATTGTTATGNCNTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAG                         TTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT
genomic: TCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTT

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

ATATACCTTACTTTAAGGAGGTCATTGTTATGGCCTCGAGTTGTGATGTATGCGGATACAAGAATTCGGAGgcaagttcag ... aattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTTATCAAATCTGTGAGGGATCTTTCTAGGGATGTTATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagctcaaaaattatagtcttaacatctcttcattgggtgtaaaattgttcagTTAAAACCCGGTGGGAGAATTCCAGAGAAAGGAAAGAAAATTAGACTCGTTATCAAATCTGTGAGGGATCTTTCTAGGGATGTTATTAAG
                   tcttaac  putative branch site (score: 5)
        aaaaattatagtctta  TA-rich tract