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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagtattcgtcttcaatttgcttgcatgcctcttttctagctggattgggtattgaagctttaatgtagaattatagggtttagagtgccggagttgtttgttgttttctttttttcattgagtcattttctgatgtgaggagtgctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG

Basic information

species Physcomitrella patens
transcript PP1S2_667V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_667V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
gtacaagtattcgtcttcaatttgcttgcatgcctcttttctagctggattgggtattgaagctttaatgtagaattatagggtttagagtgccggagttgtttgttgttttctttttttcattgagtcattttctgatgtgagga-gtgctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG
                                                                     || |   | | |  || | | |        ||   || |||    || |   || |     |    ||| |  |  | ||   || |||||||||||||||| |||||| |||| || ||||||||||| || |||||| || |  | || |||||||||||  | || ||
---------------------------------------------------------------------gtggg--tgtggttttcacaatcatttgaatgcacgt-gttgaaattatgatatagtactgtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: PP1S2_667V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ20182 (Selaginella moellendorffii), 3'ss of exon 3
gtacaagtattcgtcttcaatttgcttgcatgcctcttttctagctggattgggtattgaagctttaatgtagaattatagggtttagagtgccggagttgtttgttgttttctttttttcattgagtcattttctgatgtgaggagtgctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG
                                                                                           |         | ||     | |  || |  |  ||||  | |    ||    |   |   || |  ||||||| ||||||||||||||||| || ||||| || || ||||||||| | |   |||||||||| || ||||| |||||
-------------------------------------------------------------------------------------------gtaaattccttgtgaaagctgcgattgtgaaacgagttctctgactat-cacgttctttcttttatagATCTTCAATGGGGTGTTCATGAAGGTGAACAAGGCAACCATGAACATGCTCAAGAGAGTCGAGCCGTACGTGACTTACGG

upper sequence: PP1S2_667V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 3
gtacaagtattcgtcttcaatttgcttgcatgcctcttttctagctggattgggtattgaagctttaatgtagaattatagggtttagagtgccggagttgtttgttgttttctttttttcattgagtcattttctgatgtgaggagtgctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG
                                                                                           |         | ||    || |  || |     ||||  | ||   ||   |    | |||| |  ||||||| ||||||||||||||||| || ||||| || || ||||||||| | |   |||||||||| || ||||| |||||
-------------------------------------------------------------------------------------------gtaaattccttgtgaaagttgcgattgtgatacgagttctcttactatcacattctttcttt-tatagATCTTCAATGGGGTGTTCATGAAGGTGAACAAGGCAACCATGAACATGCTCAAGAGAGTCGAGCCGTACGTGACTTACGG

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|208376427|gb|DC902738.1|DC902738
EST:     ACATGCATCCCAAGACCAGGAAGATCATGCAGTTGTTACGTTTGAGACAG                         ATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTG
genomic: ACATGCATCCCAAGACCAGGAAGATCATGCAGTTGTTACGTTTGAGACAGgtacaagtat ... ctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTG
EST: gi|162220043|gb|FC396520.1|FC396520
EST:     ACATGCATCCCAAGACCAGGAAGATCATGCAGTTGTTACGTTTGAGACAG                         ATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTG
genomic: ACATGCATCCCAAGACCAGGAAGATCATGCAGTTGTTACGTTTGAGACAGgtacaagtat ... ctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttttctttttttcattgagtcattttctgatgtgaggagtgctttatgcagATCTTTAATGGGGTGTTCATGAAAGTTAACAAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG
                            ttctgat  putative branch site (score: 3)
     tttctttttttcatt  TA-rich tract