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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgtctttgcttggttctacgacaaaattaatgccgctattcctgtgatgttgtacacgtcctgaccgcatgctatttgttgcaatggtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGGAGGAGTCCAGTGATGAGGAGTTGAGTGACGAAGAAGATTGCATGTCAAG

Basic information

species Physcomitrella patens
transcript PP1S161_122V6.1
intron # 5
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|162275850|gb|FC451411.1|FC451411
EST:     TGCTGCGTTGATGATGCGAGACCGCGAGCATTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
genomic: TGCTGCGTTGATGATGCGAGACCGCGAGCATTATGAGCAGAAAGTGAAAGgtgactactt ... gtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
EST: gi|162154432|gb|FC330434.1|FC330434
EST:     GAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
genomic: GAGCAGAAAGTGAAAGgtgactactt ... gtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
EST: gi|162203744|gb|FC378619.1|FC378619
EST:     TGCTGCGTTGATGATGCGAGACCGCGAGCATTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
genomic: TGCTGCGTTGATGATGCGAGACCGCGAGCATTATGAGCAGAAAGTGAAAGgtgactactt ... gtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
EST: gi|7207271|gb|AW561274.1|AW561274
EST:     TGCTGCGTTGATGATGCGAGACCGCGAGCATTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
genomic: TGCTGCGTTGATGATGCGAGACCGCGAGCATTATGAGCAGAAAGTGAAAGgtgactactt ... gtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
EST: gi|162275849|gb|FC451410.1|FC451410
EST:     GAGCATTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG
genomic: GAGCATTATGAGCAGAAAGTGAAAGgtgactactt ... gtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgatgttgtacacgtcctgaccgcatgctatttgttgcaatggtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGGAGGAGTCCAGTGATGAGGAGTTGAGTGACGAAGAAGATTGCATGTCAAG
                 tcctgac  putative branch site (score: 2)
                               tatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgtctttgcttggttctacgacaaaattaatgccgctattcctgtgatgttgtacacgtcctgaccgcatgctatttgttgcaatggtgattgcagAATATTGTGAAAGATATGCCAAAGCAGAGGACATTGGAAGGCGTCCAGAGGAGGAGTCCAGTGATGAGGAGTTGAGTGACGAAGAAGATTGCATGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca