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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataattttattgacagtgtgaatgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA

Basic information

species Physcomitrella patens
transcript PP1S2_204V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_204V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataat-tttattgacagtgtgaa--tgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA
                                                                                                 |  ||||  ||| |  |  ||   |||| |     |  ||    | ||  |  | |||| |   |  |      |  |  ||      |   ||| | |||| || |||||||| |  ||| || | ||||||||||| ||||||||||| ||||| || || |||||||| || |  ||||||||||| || |||||  
-------------------------------------------------------------------------------------------------aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG

upper sequence: PP1S2_204V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 2
gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataattt-tattgacagtgtgaatgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA
                                                                                                              |||  || | ||  ||    | | |    | |   |  |  | | ||     |   |  | | |   |   ||  ||||||| |||| || ||||||||    ||  || | ||||||||||| ||||| ||||| ||||| || ||||||||||| || | ||| ||||| |||||||| ||  
-------------------------------------------------------------------------------------------------------------gtaagtccactttggaagcaatgtggggcatttttttttatacagattccaataggtttataatttagaaaatgggtgtattgtagGTCCCGATTGGAGGGTCATATAGGCTGATTGATGTGCCAATGAGCAACTGCATCAACAGTGGAATCAACAAGGTCTACATTCTCACTCAATTCAATTCAG

upper sequence: PP1S2_204V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataattttattgaca-gtgtgaatgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA
                                                                                                 | | || ||  | || | | |   |     |   ||  |  ||||| || ||| |             ||||| ||    | |||||   |  |  ||||||||||||| ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| ||||||  ||||||| | ||||| || ||||||||  
-----------------------------------------------------------------------------------------------gtatg-atcgagagctacaccttttcttcctctcctttctcgtgtgtgtattaactc-------------ctcgtcacac--actttgt---tcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG

upper sequence: PP1S2_204V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 2
gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataattttattgacagtgtgaatgaaccctggttagtgaaaactcgtgactgta-attttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA
                                                                                                        | ||| |  |       || |  |||  |  |  ||        | |  ||  ||   |||||        | | |||||   |  |  ||||||||||||| ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| |||||   ||||||| | ||||| || ||||||||  
--------------------------------------------------------------------------------------------------------gtatgatcgaga---gctacaccttttcttcctctgctt----tctcgtgtgtgtattaactccccgtcacacactttgt---tcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAATCGAGTTTTCGTACTCACGCAGTTCAACTCGG

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|162185891|gb|FC360991.1|FC360991
EST:     CTCTTACAAAGAGACGTGCCAAACCTGCT                         GTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGT
genomic: CTCTTACAAAGAGACGTGCCAAACCTGCTgtaagcccct ... tgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA
                                   taattttgtatgtatt  TA-rich tract