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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagacacttcatcagaacatgtctaaacctgaaactgatctgctcattctggcaatatcattattttatgacaccattacatattttgtcggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGTTCACCGTGACCGTAGTCGAAGAGGTATTCATCGGAGCGTCAGTCGTAGC

Basic information

species Physcomitrella patens
transcript PP1S41_63V6.1
intron # 13
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|67570334|gb|BJ943158.1|BJ943158
EST:     TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
EST: gi|162167023|gb|FC342485.1|FC342485
EST:     GAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: GAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
EST: gi|162164479|gb|FC341072.1|FC341072
EST:     TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
EST: gi|162171730|gb|FC348191.1|FC348191
EST:     TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
EST: gi|162258106|gb|FC433888.1|FC433888
EST:     TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
EST: gi|67693607|gb|BJ953840.1|BJ953840
EST:     TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
EST: gi|162159466|gb|FC336255.1|FC336255
EST:     TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAG                         ACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT
genomic: TGGAGCCCAAGACGATACAGAAGTCCTCCAAGAGCCCGATCACCACCCAGgtaagatctc ... ggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctggcaatatcattattttatgacaccattacatattttgtcggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGTTCACCGTGACCGTAGTCGAAGAGGTATTCATCGGAGCGTCAGTCGTAGC
        aatatcattattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagacacttcatcagaacatgtctaaacctgaaactgatctgctcattctggcaatatcattattttatgacaccattacatattttgtcggttactcagACACAGGAGGACTGCCAGCAGAAGCTTAAGTCGAAGTCGTAGTCCTCGTGTTCACCGTGACCGTAGTCGAAGAGGTATTCATCGGAGCGTCAGTCGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG