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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaacaatctagtctgcctcaaattccgatccttcttgcttcgttctcacgcatggaatagaatgttggccttcattgtgcatccgtgtaattatttttatgtttcatgctggcagaagcttgttagtaagggtaatggtctgacatgaaggttgcgtaatgtgatttagcagGTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCTGGCGTTGGTTCCTATGACCTTGTCTGCAAGTGTGGATTTAACTTCTGCT

Basic information

species Physcomitrella patens
transcript PP1S9_199V6.1
intron # 6
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|162195435|gb|FC370878.1|FC370878
EST:     AGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCGAAAGCAG                       
genomic: AGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCG-AA--AGgttaacaatc ... gatttagc
EST: gi|162156717|gb|FC333560.1|FC333560
EST:     AGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCGAAAG                         GTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCT
genomic: AGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCGAAAGgttaacaatc ... gatttagcagGTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCT
EST: gi|162179661|gb|FC355719.1|FC355719
EST:     AGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCGAAAG                         GTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCT
genomic: AGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCGAAAGgttaacaatc ... gatttagcagGTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCT

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: 28 (upstream exon), 33 (downstream exon)
Score: 10

AGCCATTGGAGAAGATATGGTACTAAGTTTAGTCTCGACGGATGATCAACAGAAGTACATGCGTTATCTATTAAGATCTTACGTGGAGGACAACCGAAAGgttaacaatc ... gatttagcagGTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCTGGCGTTGGTTCCTATGACCTTGTCTGCAAGTGTGGATTTAACTTCTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgttagtaagggtaatggtctgacatgaaggttgcgtaatgtgatttagcagGTCAAGTGGTGCCCAGCACCTGGCTGTGAATATGCTGTGGAATTTCAACCTGGCGTTGGTTCCTATGACCTTGTCTGCAAGTGTGGATTTAACTTCTGCT
                    gtctgac  putative branch site (score: 10)
     ttagtaa  TA-rich tract