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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagtgttaggaaaggagctggtggataacattgtctttgtggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT

Basic information

species Physcomitrella patens
transcript PP1S69_14V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 6
--cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagtgttaggaaaggagctggtgg---ataacattgtctttgtggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
      | |   || ||   | |||     |||  |    ||  | || || ||    ||      | | ||  | |    | | ||||      ||    | ||||||| ||||| ||||||||||||||||| || ||||||||||| || || |||||||| |||||||| || || || ||||| || ||   |||  |||
tttattatatggagcttagcacact-----tgtatgccttatctatttaagatatacctttttgttgtaacttttagcttctgagattgaaaccttgtgttgtagTGCTTGTTTGCCACAGAAACATTCAGTATTGGTTTGAACATGCCTGCAAAGACTGTTGTGTTTACCAATGTGCGAAAATTTGACGGTGATCGATTCAGAT

upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 6
cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagtgttaggaaaggagctggtggataac--attgtctttg-----tggtgg-gcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
        |     || |  | |   ||| ||  ||   |  |  ||| |    || |  |    |  |   |  ||  |    ||   ||      |||||    |||| || ||||| ||||||||||||||||| || ||||||||||| || || |||||||| |||||||| || || || ||||| || |||  |||  |||
-------cttccactgag-cattttagatatgttttctttctatctcaagactatgctgtgtgctgtacctttttatttcttgctgaaattaaaacatggtgttatagTGTTTGTTTGCCACAGAAACATTCAGTATTGGTTTGAACATGCCTGCAAAGACTGTTGTGTTTACCAATGTGCGAAAATTTGACGGAGACCGATTCAGAT

upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagt--gttaggaaaggagctggtggataacattgtctttgtggtggg-------------cagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
           ||   || ||   || | ||| |    ||    | | | ||   || | |||| |  || | |        | ||    |  |||| |  ||  ||  |              |||| || ||||||||||| ||||| ||||| || ||||||||||| || || || |||||||||||||| || |||||||||||||| ||||| || || |
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgtt-atgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT

upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 6
-----cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagtgttaggaaaggagctggtggataacattgtctttgtggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
         | | |    |     |    |  |||     | | | | | | |  ||| | ||      |    |     ||   | ||| ||  |       |||| || ||||| ||||| || ||||| || || |||||||||||||| || ||||| || ||||| || |||||||| ||||||||||| |||||| |||
aaaattagaatattctagtcaccgtttgtccaatggtgaatccttgctaattaattaaattttttaggtgtgctttaaatattgaaatgttttcctt-----tagTGTTTGTTTGCCACAGAGACTTTCAGCATTGGTTTGAACATGCCAGCAAAGACTGTAGTGTTTACAAATGTTCGTAAATTTGATGGGGATAAATTTAGAT

upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ21372 (Selaginella moellendorffii), 3'ss of exon 6
cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagtgttaggaaaggagctggtggataacattgtctttgtggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
                                                      | || |   ||    | ||   |  |   ||  |||      ||||||| | ||||| ||||| ||||||||||| ||  |||| ||||| ||||| || || || || || |||||||| ||||||||||| ||||| ||||| |
---------------------------------------------------gtatatttgtgcagcgtttcgtttcttcctaagttgttggatgttgcagTGCCTGTTTGCTACAGAGACATTCAGTATTGGACTGAATATGCCTGCCAAGACAGTCGTGTTCACGAACGTTCGCAAGTTTGATGGTGACAAGTTTCGCT

upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ23732 (Selaginella moellendorffii), 3'ss of exon 6
cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagtgttaggaaaggagctggtggataacattgtctttgtggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
                                                      | || | | ||    | ||   |  |   ||  |||      ||||||| | ||||| ||||| ||||||||||| ||  |||| ||||| ||||| || || || || || |||||||| ||||||||||| ||||| ||||| |
---------------------------------------------------gtatatttgtacagcgtttcgtttcttcctaagttgttggatgttgcagTGCCTGTTTGCTACAGAGACATTCAGTATTGGACTGAATATGCCTGCCAAGACAGTCGTGTTCACGAACGTTCGCAAGTTTGATGGTGACAAGTTTCGCT

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|162156045|gb|FC332212.1|FC332212
EST:     CAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAG                         TGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAA
genomic: CAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgctt ... tggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggtaagtgttaggaaaggagctggtggataacattgtctttgtggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT
                            ggataac  putative branch site (score: 3)
                                       tctttgt  putative PPT
                              ataacatt  TA-rich tract