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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGAACAAACATTCGACCACTTTGGGGAACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaatctcctactggcgtattacctcaatcgtcaattcattttattacccattaataaatcccttttaattaaattcgatcatgaactttatgataagtaatttatgcattttcgtttcatgacatgagattcacagtatttgttgtgatattttctatgctgtttcttgcag

Basic information

species Physcomitrella patens
transcript PP1S180_53V6.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ07726 (Selaginella moellendorffii), 5'ss of exon 6
--------------------GAGGGAACAAACATTCGACCACTTTGGGGAACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaatctcctactggcgtattacctcaatcgtcaattcattttattacccattaataaatcccttttaattaaattcgatcatgaactttatgataagtaatttatgcattttcgtttcatgacatgagattcacagtatttgttgtgatattttctatgctgtttcttgcag
|| || ||| |||| | || || |||||||| || |||||||||||||||||| | ||||||||||| || || || |||| | | | | || | || || ||| || | | | ||| | || ||
CTTTAGCTAAGCAGCTACAGGAAGGCACAGACATCAGGCCTCTCTGGGGAACCGCGCAGCTTTTCAAGCACCCAAGATACATGCATGGCGCGGCCACCAGgtattag-attttcttgttgctcgctttcct--attat--aattgtttcttcccctggtag----------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ07670 (Selaginella moellendorffii), 5'ss of exon 6
--------------------GAGGGAACAAACATTCGACCACTTTGGGGAACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaatctcctactggcgtattacctcaatcgtcaattcattttattacccattaataaatcccttttaattaaattcgatcatgaactttatgataagtaatttatgcattttcgtttcatgacatgagattcacagtatttgttgtgatattttctatgctgtttcttgcag
|| || ||| |||| |||| || |||||||| || |||||||||||||||||| | ||||||||||| || || || |||| | | | | || | || | || ||| || | | | ||| | || ||
CTTTAGCTAAGCAGCTACAGGAAGGCACAGACATCAGACCTCTCTGGGGAACCGCGCAGCTTTTCAAGCACCCAAGATACATGCATGGCGCAGCCACCAGgtattag-attttcttgttgctctctttcct--attat--agttgtttcttcccctggtag----------------------------------------------------------------------------------------------------------------------
















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|208374343|gb|DC941156.1|DC941156
EST:     ACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAG                         TCCGGACGTCCGTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGAT
genomic: ACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaa ... tttcttgcagTCCGGACGTCCGTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGAT
EST: gi|100392407|gb|BY953347.1|BY953347
EST:     CTGCCCAGCTTTTTCA-GCACCCACGTTACATGCATGGAGCTGCTACAAG                         TCCGGACGGTC-GTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGA
genomic: CTGCCCAGCTTTT-CAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaa ... tttcttgcagTCCGGACG-TCCGTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGA
EST: gi|100404244|gb|BY955328.1|BY955328
EST:     ACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAG                         TCCGGACGTCCGTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGAT
genomic: ACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaa ... tttcttgcagTCCGGACGTCCGTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGAT
EST: gi|100398077|gb|BY954076.1|BY954076
EST:     CTGCCCAGCTTTTCAAGCACCCACGGTACATGCATGGAGCTGCTACAAAG                         TCGGGACGTC-GTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGA
genomic: CTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAA-Ggtctcaacaa ... tttcttgcagTCCGGACGTCCGTGTTTATGCATATGCAGCTGCTCAGGTCAAGAAGGCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGAACAAACATTCGACCACTTTGGGGAACTGCCCAGCTTTTCAAGCACCCACGTTACATGCATGGAGCTGCTACAAGgtctcaacaatctcctactggcgtattacctcaatcgtcaattcattttattacccattaataaatcccttttaattaaattcgatcatgaactttatgataagtaatttatgcattttcgtttcatgacatgagattcacagtatttgttgtgatattttctatgctgtttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT