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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcccaagatttgttgccgtgttcgtcacatgcggaagtcttgtcgtttgcgtaatgtcagccgtgttgacgtggttatgtttttacgccatcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGTGGTTCTGGACACAGGAAGTGACCTGCTATGGATCCCCTGTGAGTGTGAG

Basic information

species Physcomitrella patens
transcript PP1S6_43V6.1
intron # 1
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|67569425|gb|BJ942249.1|BJ942249
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
EST: gi|67508313|gb|BJ941182.1|BJ941182
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
EST: gi|18327766|gb|BJ159770.1|BJ159770
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
EST: gi|18328211|gb|BJ160215.1|BJ160215
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
EST: gi|18328546|gb|BJ160551.1|BJ160551
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
EST: gi|67703897|gb|BJ964130.1|BJ964130
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACA
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACA
EST: gi|67572575|gb|BJ945399.1|BJ945399
EST:     CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGG                         ATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT
genomic: CAGTACGTTCTCATCCAGGGAAATGCCACAGAGCAGCTGTTCGGAGGAGGgtgagtttct ... tcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcgtaatgtcagccgtgttgacgtggttatgtttttacgccatcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGTGGTTCTGGACACAGGAAGTGACCTGCTATGGATCCCCTGTGAGTGTGAG
                  tgttgac  putative branch site (score: 3)
                             ttatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcccaagatttgttgccgtgttcgtcacatgcggaagtcttgtcgtttgcgtaatgtcagccgtgttgacgtggttatgtttttacgccatcacatgcagATTACACTATAGTTACATAGACATTGGGACTCCAAACGTGCAGTTTTTGGTGGTTCTGGACACAGGAAGTGACCTGCTATGGATCCCCTGTGAGTGTGAG

- - - - - - - - - - - - -cacatgc