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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattgattatgtactcaagactttgtcttattatatttacattttttatgtagttatgcatcgtgtatactgtcttacaacggtgaatatcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGACGTGGGCGATAGTTTGTGGTTCATATCCCTCATTAGGGTTTCCAGTGTTG

Basic information

species Physcomitrella patens
transcript PP1S37_118V6.1
intron # 3
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|162210344|gb|FC386224.1|FC386224
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208364908|gb|DC947050.1|DC947050
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|37824593|gb|BJ582659.1|BJ582659
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|162210343|gb|FC386223.1|FC386223
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|18345230|gb|BJ177271.1|BJ177271
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|162217222|gb|FC391962.1|FC391962
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208375129|gb|DC956469.1|DC956469
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208369557|gb|DC932539.1|DC932539
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|162217223|gb|FC391963.1|FC391963
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208388874|gb|DC932902.1|DC932902
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC

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: 32 (upstream exon), 12 (downstream exon)
Score: 4

GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGACGTGGGCGATAGTTTGTGGTTCATATCCCTCATTAGGGTTTCCAGTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtagttatgcatcgtgtatactgtcttacaacggtgaatatcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGACGTGGGCGATAGTTTGTGGTTCATATCCCTCATTAGGGTTTCCAGTGTTG
                           gtcttac  putative branch site (score: 4)
      tagttat  TA-rich tract