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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacgtagtaagtttttctcataatttatgttgataaccgtacaaagggtgaattgaatacagcactagttgagttggaggtaataaaggtgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCCGACCAACGAGGACGAGCAATCAAAATTAATCGACACTATCCAG

Basic information

species Physcomitrella patens
transcript PP1S93_161V6.1
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|162195161|gb|FC368823.1|FC368823
EST:     TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
EST: gi|67695546|gb|BJ955779.1|BJ955779
EST:     TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
EST: gi|162182993|gb|FC360559.1|FC360559
EST:     CGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: CGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
EST: gi|67573920|gb|BJ946744.1|BJ946744
EST:     TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
EST: gi|67697308|gb|BJ957541.1|BJ957541
EST:     TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
EST: gi|162195160|gb|FC368822.1|FC368822
EST:     TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
EST: gi|67572179|gb|BJ945003.1|BJ945003
EST:     TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTG                         GTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC
genomic: TATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCC

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), 34 (downstream exon)
Score: 16

TGCGGAGCCCTTCCTCGTCGCCTGAACCGCTTGTGTGGACCCCGGAGTTTTATGACGAGCTCCAGAATACGATTGGCGGAGGGAAGCCTAAAATGCGTTGgtgggtctcc ... tgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCCGACCAACGAGGACGAGCAATCAAAATTAATCGACACTATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggtgaattgaatacagcactagttgagttggaggtaataaaggtgcattacagGTACTTTAACAGACACGGATGGCCGACGTCTACCATCTTGCCAAACGCTCCGACCAACGAGGACGAGCAATCAAAATTAATCGACACTATCCAG
      aattgaata  TA-rich tract