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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggagcgtaggcatctcggaagtattgtatgctgtgaatatttaactggagcacaattttcttacgtctcagctttgttgcgatttctttcatgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTCGAACCGTTGGCTTCACACCCGCCTACTTCTGAATATCCAACAA

Basic information

species Physcomitrella patens
transcript PP1S490_9V6.1
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|18345768|gb|BJ177811.1|BJ177811
EST:     TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGG                         ACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
genomic: TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGGgtaatttttt ... catgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
EST: gi|100452446|gb|CJ975275.1|CJ975275
EST:     TTGCCAGTTGCTGGACCCAGCTTATCGATGTCNAGCAAGACGATGGAAGG                         ACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
genomic: TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGGgtaatttttt ... catgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
EST: gi|100372742|gb|BY948681.1|BY948681
EST:     TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGG                         ACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
genomic: TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGGgtaatttttt ... catgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
EST: gi|208355697|gb|DC910519.1|DC910519
EST:     TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGG                         ACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCANGTC
genomic: TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGGgtaatttttt ... catgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
EST: gi|100357347|gb|BY983812.1|BY983812
EST:     TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGG                         ACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC
genomic: TTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGGgtaatttttt ... catgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTC

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: 34 (upstream exon), 33 (downstream exon)
Score: 13

TGGAGGGGAATGGTTGACATGGAATCAGCTTATGCCTGAAGAGGACGTTATTGCCAGTTGCTGGACCCAGCTTATCGATGTCGAGCAAGACGATGGAAGGgtaatttttt ... catgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTCGAACCGTTGGCTTCACACCCGCCTACTTCTGAATATCCAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggagcacaattttcttacgtctcagctttgttgcgatttctttcatgtcacagACCTTGAACCAATCCATAAAGTATGTGCCACTTCAGACGCCCCTTCAGGTCGAACCGTTGGCTTCACACCCGCCTACTTCTGAATATCCAACAA
             ttcttac  putative branch site (score: 13)
                                      tttctttcat  putative PPT
         aattttctta  TA-rich tract