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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtttggacacatactcaacatcctcagctccaaatttttctctacttaatcccttatatgcgtacaaaaatccctatctaacgtctcgactgtgttgatgatttgctggaattgatgttaaacatgcgcatcacctattcttgtacgctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGGTTTACGCGCTTCTCTTTCCTTGGAATCGACCTCTCAAGCGATGGCCACA

Basic information

species Physcomitrella patens
transcript PP1S80_36V6.1
intron # 7
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|162172906|gb|FC348911.1|FC348911
EST:     GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTG                         ATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
genomic: GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTGgtgcgtttgg ... gctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
EST: gi|162199436|gb|FC374063.1|FC374063
EST:     GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTG                         ATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
genomic: GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTGgtgcgtttgg ... gctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
EST: gi|162257551|gb|FC433685.1|FC433685
EST:     GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTG                         ATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
genomic: GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTGgtgcgtttgg ... gctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
EST: gi|208348444|gb|DC913186.1|DC913186
EST:     GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTG                         ATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG
genomic: GCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTGgtgcgtttgg ... gctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGG

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), 24 (downstream exon)
Score: 8

CGCATTGGGCTTCAACCCTCCAGACCCAGACATTATGAAGAAGCCTCCGCGCAAGAGCACTGATGTCCTCATCAACTCGTGGGTACTCCTGCGTTACCTGgtgcgtttgg ... gctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGGTTTACGCGCTTCTCTTTCCTTGGAATCGACCTCTCAAGCGATGGCCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctggaattgatgttaaacatgcgcatcacctattcttgtacgctttcgcagATTATTGGCTTATACGTTGGAATTGCCACTGTTGGTGCGTTCTCTCTGTGGTTTACGCGCTTCTCTTTCCTTGGAATCGACCTCTCAAGCGATGGCCACA
        aattgat  putative branch site (score: 8)
                                            cgctttc  putative PPT
             atgttaaa  TA-rich tract