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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttcgatactccactttctttttaggatatcttgtatttatctttatgcagcatgctttgtgatttaactccaattttacagttcttccgcccctgactgtgatggaggtgcattgtttagctggattgtgatagaggattttaactggacatgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACATAGCATGGTTTACACCAGTGGAAGTTTTCCAG

Basic information

species Physcomitrella patens
transcript PP1S199_22V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_22V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 3'ss of exon 2
gcaagttcgatactccactttctttttaggatatcttgtatttatctttatgcagcatgctttgtgatttaactccaattttacagttcttccgcccctgactgtgatggaggtgcattgtttagctggattgtgatagaggattttaactggacatgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACATAGCATGGTTTACACCAGTGGAAGTTTTCCAG
                                               ||   |  |||   ||||     || | | ||| |   ||| | | |      | | |  ||||       | |||  || ||     |  || |   ||  ||        || |||  ||  ||| || |   ||||  |   ||||||||||||| |||||||||| || ||||| || ||||||||  | ||| ||
--------------------------------------------ctgttgaactccattgattgtttgccaattacgattctgt-gttgtgctgtttt--aatatcttgga-------tatttgactaga----aacggaagtaatttgctta------tgtagGTAGGAGTGCGTATATGCAGTACCTTGATAAGTTGTACAAGAAGCATGACATCGCTTGGTTCACTCCAGTGGAGCTCTTCAAG

upper sequence: PP1S199_22V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G14130.1 (Glycine max), 3'ss of exon 2
gcaagttcgatactccactttctttttaggatatcttgtatttatctttatgcagcatgctttgtgatttaact---ccaattttacagttcttccgcccctgactgtgatggaggtgcattgtttagctggattgtgatagaggattttaactggacatgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACATAGCATGGTTTACACCAGTGGAAGTTTTCCAG
                                                   || |   | ||    |  | |||    |||||| ||| |  ||    |  | | | |  ||    ||  ||||    ||    |||  |||||   |       ||||| || |||| |||   ||||| |   |||| |||  |||  | |||||||||  ||||||| |||||||||||||||||||| ||||  ||
---------------------------------------------------gctgttagtttaagaagctgactaactcaatttaacactgattataactttaaattttctg----tggtttgt---actca--tgtagtagagtggt-------gacatatttcagGCCGGAAAGCTTATATGAAGTACTTGGATAATATTTACAAGCAGAGTGACATATCATGGTTTACACCAGTGGAACTTTTTAAG
















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|100352093|gb|BY964702.1|BY964702
EST:     TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAG                         GACGGGCTGCTTACAACAAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
genomic: TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAGgcaagttcga ... catgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
EST: gi|18353878|gb|BJ185933.1|BJ185933
EST:     TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAG                         GACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
genomic: TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAGgcaagttcga ... catgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
EST: gi|18350048|gb|BJ182099.1|BJ182099
EST:     TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAG                         GACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
genomic: TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAGgcaagttcga ... catgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
EST: gi|100395236|gb|BY953648.1|BY953648
EST:     TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAG                         GACGGGCTGCTTACAACGAGTATTTGAGTAAGCTGTACAAGCAGCATGACA
genomic: TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAGgcaagttcga ... catgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
EST: gi|100448323|gb|CJ972622.1|CJ972622
EST:     TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAG                         GACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA
genomic: TAATGCAGTTGGCGCCATAGCAGAGCCAATCAGGTTCGATCGCATCCCAGgcaagttcga ... catgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggtgcattgtttagctggattgtgatagaggattttaactggacatgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACATAGCATGGTTTACACCAGTGGAAGTTTTCCAG
                                  ttttaac  putative branch site (score: 2)
                                 attttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttcgatactccactttctttttaggatatcttgtatttatctttatgcagcatgctttgtgatttaactccaattttacagttcttccgcccctgactgtgatggaggtgcattgtttagctggattgtgatagaggattttaactggacatgttgcagGACGGGCTGCTTACAACGAGTATTTGAGTAAGTTGTACAAGCAGCATGACATAGCATGGTTTACACCAGTGGAAGTTTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG