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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctaaggctcatgaatgtgaaatcaagtatgcttggaaatgttttatatctgttgtcagtgctcactttatgtcgtgtggttatttaattgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACATTGGGGACTTCTATACTGGTGTTTACACGAACGGGCTTTATGGCTCTGT

Basic information

species Physcomitrella patens
transcript PP1S318_21V6.1
intron # 8
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|162223833|gb|FC400087.1|FC400087
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|18339668|gb|BJ171695.1|BJ171695
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|162223832|gb|FC400086.1|FC400086
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|208351340|gb|DC922091.1|DC922091
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATNTCATGCCACTTTAATGTCAANTACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|37829503|gb|BJ587515.1|BJ587515
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|162256309|gb|FC432319.1|FC432319
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|18337336|gb|BJ169360.1|BJ169360
EST:     GGAGGCCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATAC
genomic: GGAGG-CCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATG-AGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATAC
EST: gi|208348104|gb|DC916914.1|DC916914
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|162155346|gb|FC331245.1|FC331245
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|162202021|gb|FC377227.1|FC377227
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|18337218|gb|BJ169242.1|BJ169242
EST:     CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
EST: gi|208363112|gb|DC954326.1|DC954326
EST:     CTTGGTCGAGCCTTTAAG                         ACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA
genomic: CTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACA

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: 31 (upstream exon), 33 (downstream exon)
Score: 14

TCCTTTGAAAGCTGTGCGAGTGATGCACACTGTGGCCATGCGCACAGAAGCAACCATGCCAGAGGAGGAGGCCCCTGCTAACCTTGGTCGAGCCTTTAAGgtaactgctt ... ttgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACATTGGGGACTTCTATACTGGTGTTTACACGAACGGGCTTTATGGCTCTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatctgttgtcagtgctcactttatgtcgtgtggttatttaattgaggacagACTCATATGAGTGAAATGTTCGCATTTCATGCCACTTTAATGTCAAATACATTGGGGACTTCTATACTGGTGTTTACACGAACGGGCTTTATGGCTCTGT
                                     ttatttaattga  TA-rich tract