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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagttcaactatttttgtatcctttcattgttaactttggtagaagacagtgctttcctttggcctatgttgccattgtggtacgtggttttctatgcatgacttttgtgatatctttgatgaatgtccaaactggtattgcttaagtgtgatgttggacgtggagttcatttcatttacatatttttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACAAGGCGGGAAAGCTTATCGGAAGCCAG

Basic information

species Physcomitrella patens
transcript PP1S137_89V6.1
intron # 3
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|67695499|gb|BJ955732.1|BJ955732
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208364746|gb|DC954476.1|DC954476
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|37828269|gb|BJ586281.1|BJ586281
EST:     CTCGTCAAGATNTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGNNNNNNNCTGAGAATGGGTTGGTTGCCCAC
genomic: CTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACG-TTTTTTCTGAGAATGGGTTGGTTGCCCAC
EST: gi|208370169|gb|DC944394.1|DC944394
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208386575|gb|DC952770.1|DC952770
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208347945|gb|DC921202.1|DC921202
EST:     GATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: GATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208368085|gb|DC947645.1|DC947645
EST:     TGTGGGA-GTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|37834823|gb|BJ592835.1|BJ592835
EST:     CTCAGANCAACTTGGGAAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCAC
genomic: CTCAGAACAACTTGGG-AAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCAC
EST: gi|208362674|gb|DC947165.1|DC947165
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208380771|gb|DC919459.1|DC919459
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208357863|gb|DC918625.1|DC918625
EST:     ATCTCGTCAAGATCTCAGAACAACTTGGGAAAGCTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: ATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208360951|gb|DC946640.1|DC946640
EST:     TGTGGGAGGTTCGGATCTCGTCNAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208346101|gb|DC917054.1|DC917054
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208366441|gb|DC947609.1|DC947609
EST:     G-GGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGNAAAACTG                         CTGTTACGGATTACGACTACGNNNNNNNCTGAGAATGGGTTGGTTGCCCA
genomic: GTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGG-AAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACG-TTTTTTCTGAGAATGGGTTGGTTGCCCA
EST: gi|208385973|gb|DC956811.1|DC956811
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|162250055|gb|FC427364.1|FC427364
EST:     TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208358539|gb|DC946500.1|DC946500
EST:     CGTCAAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: CGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208360140|gb|DC950169.1|DC950169
EST:     ATCTCGTCNAGATCTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: ATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|208399394|gb|DC924824.1|DC924824
EST:     CGTCNAGATTTCAGAACAACTTGGGAAAACTG                         CTGTTACGGATTACGANTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: CGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|162208934|gb|FC385278.1|FC385278
EST:     GATCTCGTCAAGATCTCAGAACAAC-TGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: GATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
EST: gi|37844701|gb|BJ602709.1|BJ602709
EST:     CAGAACAACTTGGGAAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCAC
genomic: CAGAACAACTTGGG-AAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCAC
EST: gi|37826210|gb|BJ584222.1|BJ584222
EST:     TCAGANCAACTTGGGAAAACTG                         CTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA
genomic: TCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACA

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: 25

GTGGTCACCATAGGTGTTGTGGGAGGTTCGGATCTCGTCAAGATCTCAGAACAACTTGGGAAAACTGgtacagttca ... ttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACAAGGCGGGAAAGCTTATCGGAAGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaagtgtgatgttggacgtggagttcatttcatttacatatttttccctgcagCTGTTACGGATTACGACTACGTTTTTTCTGAGAATGGGTTGGTTGCCCACAAGGCGGGAAAGCTTATCGGAAGCCAG
                                        tatttttccct  CT-rich tract
                         ttcatttcatttacat  TA-rich tract