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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcgctcagagtttcaagctttgggggcattagtttttgtttctcaatatgaaaaattaacttttgtttggtttcatgggttgaatgtaatgtcctccgaagtatgcaaccagcatgatggcaagatggataattcgaacaggtgtgtcttcttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCAAAGAAGACCGAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACT

Basic information

species Physcomitrella patens
transcript PP1S47_72V6.1
intron # 2
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|162237338|gb|FC412446.1|FC412446
EST:     CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|67726911|gb|BJ977170.1|BJ977170
EST:     CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|162237337|gb|FC412445.1|FC412445
EST:     GGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: GGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|18362523|gb|BJ194594.1|BJ194594
EST:     GGATCCGGCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: GGATCCGGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|162224246|gb|FC399505.1|FC399505
EST:     GGCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: GGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|37839797|gb|BJ597805.1|BJ597805
EST:     GTCGGCACACATGTTATTNCAG                         GTTGCCAAGCACGTCCTTCAAGGGCTGCTCACGTAACAACAACAGGAAGT
genomic: GTCGGCACACATGTTATT-CAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCC-TCAA-GGCTGCTCACGTAACAACAACAGGAAGT
EST: gi|37839869|gb|BJ597877.1|BJ597877
EST:     TCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: TCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|162196625|gb|FC374915.1|FC374915
EST:     CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACTACA-CAGGAAGTTCA
genomic: CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|67697068|gb|BJ957301.1|BJ957301
EST:     GCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: GCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|37846181|gb|BJ604189.1|BJ604189
EST:     CACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGGCTGCTCACGTAACAACAACAGGAAAGTT
genomic: CACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAA-GGCTGCTCACGTAACAACAACAGG-AAGTT
EST: gi|37835120|gb|BJ593132.1|BJ593132
EST:     CACACATGTTATTCAG                         GTTGCCAAGCACGTCNTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: CACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
EST: gi|162224247|gb|FC399506.1|FC399506
EST:     CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAG                         GTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA
genomic: CGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCA

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: 30 (upstream exon), 31 (downstream exon)
Score: 19

CCTCACCGCTACCGAAGGACTCCAGAAAGCTGGCTGCGAAGAAGGCAAGACGGTGCTTGTTCTTGGTGGATCCGGCGGAGTCGGCACACATGTTATTCAGgttattttcg ... ttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCAAAGAAGACCGAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccagcatgatggcaagatggataattcgaacaggtgtgtcttcttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCAAAGAAGACCGAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACT
                                           tcttgat  putative branch site (score: 19)
                                      tgtcttctt  CT-rich tract
                      ataatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattttcgctcagagtttcaagctttgggggcattagtttttgtttctcaatatgaaaaattaacttttgtttggtttcatgggttgaatgtaatgtcctccgaagtatgcaaccagcatgatggcaagatggataattcgaacaggtgtgtcttcttgattgcagGTTGCCAAGCACGTCCTCAAGGCTGCTCACGTAACAACAACAGGAAGTTCAAAGAAGACCGAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG