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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtaatgtatatcctaatcacgagccagttgagaatctatgctaatttaagataggtaatcaactgcgattgaagttctaaggtggttttttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGGCGGCTATACCGATGGAGTTCGCGGCAGTTAACGGATTGCGAGGTGCCAC

Basic information

species Physcomitrella patens
transcript PP1S146_17V6.3
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|67575280|gb|BJ948104.1|BJ948104
EST:     CCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTTCGCTGTGGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATG
genomic: CCACACTGTCTTCCCTCTCTCTTCTCGCTCCACAC-TCGCTGT-GTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATG
EST: gi|162220399|gb|FC395754.1|FC395754
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|162158539|gb|FC334542.1|FC334542
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGCATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|208394235|gb|DC933903.1|DC933903
EST:     GTCTTCCCTCTCTCTTCTCGCTCCACACTTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: GTCTTCCCTCTCTCTTCTCGCTCCACAC-TCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|67507633|gb|BJ940513.1|BJ940513
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|67576312|gb|BJ949136.1|BJ949136
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100364909|gb|BY947969.1|BY947969
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100444048|gb|BY963946.1|BY963946
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|162181623|gb|FC357925.1|FC357925
EST:     TTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100440863|gb|BY962351.1|BY962351
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100386266|gb|BY987933.1|BY987933
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100445755|gb|CJ970054.1|CJ970054
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|162256527|gb|FC432837.1|FC432837
EST:     CACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: CACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|162216943|gb|FC391943.1|FC391943
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100448931|gb|CJ973230.1|CJ973230
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100426446|gb|BY958902.1|BY958902
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|18343661|gb|BJ175699.1|BJ175699
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|18325821|gb|BJ157818.1|BJ157818
EST:     GCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: GCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|162188015|gb|FC365005.1|FC365005
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|18367855|gb|BJ199938.1|BJ199938
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGNATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|162241856|gb|FC418111.1|FC418111
EST:     CACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: CACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100423120|gb|BY958156.1|BY958156
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|18372829|gb|BJ204431.1|BJ204431
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
EST: gi|100411895|gb|BY992393.1|BY992393
EST:     TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCG                         GTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG
genomic: TTCCACACTGTCTTCCCTCTCTCTTCTCGCTCCACACTCGCTGTGTATCGgtaagctcta ... tttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaagataggtaatcaactgcgattgaagttctaaggtggttttttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGGCGGCTATACCGATGGAGTTCGCGGCAGTTAACGGATTGCGAGGTGCCAC
 tgctaat  putative branch site (score: 2)
                                          ttttttcttgc  putative PPT
                                          ttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtaatgtatatcctaatcacgagccagttgagaatctatgctaatttaagataggtaatcaactgcgattgaagttctaaggtggttttttcttgcagGTCAATGAATTTTTTGGGGTGAATAGGTATAACTAGAGTTCCTTGAGATGGCGGCTATACCGATGGAGTTCGCGGCAGTTAACGGATTGCGAGGTGCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA