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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatttgtgacggttttttagggttgtttgagctcttttctttctttctttctttttgtctttgtgaagctgacgtagtgttaaacgacatcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCACCCTCATCCAGATCATTTCCTGCCTGTGTTGGTTGGGTTGGGAGCTGCG

Basic information

species Physcomitrella patens
transcript PP1S426_3V6.1
intron # 3
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|162216397|gb|FC393230.1|FC393230
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|67694542|gb|BJ954775.1|BJ954775
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|208381204|gb|DC923741.1|DC923741
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|208381609|gb|DC915475.1|DC915475
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|162204471|gb|FC381699.1|FC381699
EST:     CCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: CCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|67691357|gb|BJ951590.1|BJ951590
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|67700631|gb|BJ960864.1|BJ960864
EST:     ATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: ATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|37840261|gb|BJ598269.1|BJ598269
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
EST: gi|67577756|gb|BJ949923.1|BJ949923
EST:     TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAA                         GCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA
genomic: TGGGCCAAGGCATTCGACGGATGGTTGACTGATGTGCTACTCAACAGCAAgtaagaattc ... atcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttctttttgtctttgtgaagctgacgtagtgttaaacgacatcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCACCCTCATCCAGATCATTTCCTGCCTGTGTTGGTTGGGTTGGGAGCTGCG
                       agctgac  putative branch site (score: 3)
     ttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatttgtgacggttttttagggttgtttgagctcttttctttctttctttctttttgtctttgtgaagctgacgtagtgttaaacgacatcgatgcagGCACAAGGAAGCAATGGAATGGGAGAAAGCACCATATGCTTCCAAAGCTCACCCTCATCCAGATCATTTCCTGCCTGTGTTGGTTGGGTTGGGAGCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC