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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACGTGATGTCTCATGGTGTACAAACACCTCTATCTCATGTGGCCGCAGTTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccggtatttccgaaattcgctgcttctattggttgtgttgtcaaatattgctggacctaagtgacgttgaattctttgctggacctgagtatgcagccttgtgttgcctgtctgatcttgtatttgtcatgtgtggctgaacag

Basic information

species Physcomitrella patens
transcript PP1S101_227V6.1
intron # 3
splice site 5'
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|67719423|gb|BJ969682.1|BJ969682
EST:     TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
genomic: TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
EST: gi|208399841|gb|DC904713.1|DC904713
EST:     TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
genomic: TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
EST: gi|208357815|gb|DC918605.1|DC918605
EST:     ACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
genomic: ACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
EST: gi|208360244|gb|DC950217.1|DC950217
EST:     TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
genomic: TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
EST: gi|208370405|gb|DC936411.1|DC936411
EST:     TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
genomic: TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
EST: gi|67704607|gb|BJ964840.1|BJ964840
EST:     TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCA
genomic: TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCA
EST: gi|67573448|gb|BJ946272.1|BJ946272
EST:     TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCT                         ATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC
genomic: TTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAAC

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: 30 (upstream exon), 14 (downstream exon)
Score: 2

GAACGTGATGTCTCATGGTGTACAAACACCTCTATCTCATGTGGCCGCAGTTTCGGTTTCCAATCTTGAAACATTGACAGTAATGCCATATGATACTTCTgtgagttccg ... ggctgaacagATGGTCAAAGAAGTTGAGAAAGCTATTCGAAATTCTCCACTCAAACTAAACCCCATGGCGGAAGGGGAAGTCCTGAGGGTTCCTATCCCTAA




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