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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtttaattttcagtgctctgagctagtacggtttcattttagggcttgaaactggaaaatagcgcgcttctttttactatgaatccgttcaccagcggtgttttaggtttttcggtgttttcttgcacgagtgcacattatctgattgcgttcttggcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACTTACGACTTCAAATACGGAGTCCGCGCAATCCAG

Basic information

species Physcomitrella patens
transcript PP1S28_168V6.1
intron # 4
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|100446747|gb|CJ971046.1|CJ971046
EST:     TCAGAACNCCCATTGCTGTCACCGTTCCCAACACANACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGNCTTACCGTCCTAGCCAC
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCAC
EST: gi|208358357|gb|DC934550.1|DC934550
EST:     CGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTANCCACGCANACGCCAC
genomic: CGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGA-GGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCAC
EST: gi|208390477|gb|DC933734.1|DC933734
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|67508161|gb|BJ941032.1|BJ941032
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|162159689|gb|FC336075.1|FC336075
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|100385742|gb|BY987807.1|BY987807
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|162189601|gb|FC365823.1|FC365823
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|67572551|gb|BJ945375.1|BJ945375
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|100439543|gb|BY961986.1|BY961986
EST:     TCGGGACGCCCATTGCTGTCACCGTTCCCCACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAG
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAG
EST: gi|67508549|gb|BJ941412.1|BJ941412
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|162152501|gb|FC328779.1|FC328779
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
EST: gi|162188362|gb|FC364232.1|FC364232
EST:     TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGG                         GATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT
genomic: TCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACT

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: 35 (upstream exon), 34 (downstream exon)
Score: 14

GACTTACACTCGGAACGCCCATTGCTGTCACCGTTCCCAACACAGACCAGCGGGGAGGGgtaagcgttt ... gcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACTTACGACTTCAAATACGGAGTCCGCGCAATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggtgttttcttgcacgagtgcacattatctgattgcgttcttggcttgaacagGATTACTCTGAAATTAGCGTGGCTTACCGTCCTAGCCACGCAGACGCCACTTACGACTTCAAATACGGAGTCCGCGCAATCCAG
                            atctgat  putative branch site (score: 14)
      ttttctt  TA-rich tract