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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatacttgccttgatcgggacaatgcaaccaacttgttctgtttggatgcagaagaaatacatcacatgagcggaatttctaactgtaatcgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATATCAAGCATGGTTGGGTTACTACAATTCATGTAGACTCTTAAAGTGGGACA

Basic information

species Physcomitrella patens
transcript PP1S235_69V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S235_69V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 9
------gatacttgccttgatcgggacaatgcaaccaacttgttctgtttggatgcagaagaaatacatcacatgagcggaatttctaactgtaatcgttgttcagGTGAACAAAG--CTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATATCAAGCATGGTTGGGTTACTACAATTCATGTAGACTCTTAAAGTGGGACA
      || |||  |||   |   |  |  | | |||| || |||| |  |  |    ||           |||    ||   ||  ||   |  |      ||||||| | ||||  |||    |  |    |||| || |||| |||    |||||||| |||||||||||||||||||| ||    |      |     | ||||
tctcacgaaactaacctcttttacgtta--gaagccaaatttttct-taagagtatgtaactcgagtga-gcattgatgggtgttgaaaacatgttaa--aatcagGTGCAGAAAGGGCTTATCCAAGTGGAAATGACGA-ACAAGGAG-GCGGCATATCAGGCATGGTTGGGTTACTACAAATCGCAGAAGAAGATTGCTAGAGACA
















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|37822358|gb|BJ580424.1|BJ580424
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|162278581|gb|FC454043.1|FC454043
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|37853308|gb|BJ611316.1|BJ611316
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|162278582|gb|FC454044.1|FC454044
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|37849769|gb|BJ607777.1|BJ607777
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|37834369|gb|BJ592381.1|BJ592381
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|37850758|gb|BJ608766.1|BJ608766
EST:     CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: CAATCACTCAATCCAAGGGCACGGAAGTCTCTCCGGATATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
EST: gi|67696346|gb|BJ956579.1|BJ956579
EST:     TATTGAAGCAAAG                         GTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT
genomic: TATTGAAGCAAAGgtttgtactt ... cgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcagaagaaatacatcacatgagcggaatttctaactgtaatcgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATATCAAGCATGGTTGGGTTACTACAATTCATGTAGACTCTTAAAGTGGGACA
                                ttctaac  putative branch site (score: 1)
                             aatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatacttgccttgatcgggacaatgcaaccaacttgttctgtttggatgcagaagaaatacatcacatgagcggaatttctaactgtaatcgttgttcagGTGAACAAAGCTTTGGGATATATTGATGAAGATACAAAGAGCAAAGCATATCAAGCATGGTTGGGTTACTACAATTCATGTAGACTCTTAAAGTGGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatga