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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCATCGGTAGTGGCATCCGTGAGTTTTAACGATGGGGGAGAAACTAGCGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTGgtgagatttatcggctgctcacttcagtttttatttctttctagggagtttgctgctgttagctgctcgctgatccatcgaataaatgggacattctcgg...

Basic information

species Physcomitrella patens
transcript PP1S321_30V6.1
intron # 1
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|18349143|gb|BJ181192.1|BJ181192
EST:     CGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTG                         GAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAA
genomic: CGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTGgtgagattta ... atgaatccagGAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAA
EST: gi|18355129|gb|BJ187188.1|BJ187188
EST:     CGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTG                         GAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAA
genomic: CGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTGgtgagattta ... atgaatccagGAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAA
EST: gi|18353958|gb|BJ186013.1|BJ186013
EST:     CGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTG                         GAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAA
genomic: CGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTGgtgagattta ... atgaatccagGAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAA

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), 35 (downstream exon)
Score: 20

GAATCATCGGTAGTGGCATCCGTGAGTTTTAACGATGGGGGAGAAACTAGCGACCAAATTGGCAGGCCTCGAGGCCCTCAACAACGAGACAGTCGATTTGgtgagattta ... atgaatccagGAACACATCCCTGTCGATGAGGTCTTCCAGCACTTGCGCTGTACTGAAGAAGGGCTGTCAAATGAGGAGGCTGAAGCGAGGCTTCAGATCTTCGGCTTCA




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