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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTTCGGAATGCAGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA

Basic information

species Physcomitrella patens
transcript PP1S552_1V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTTCGGAATGCAGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------
         |    ||| ||    |      |  |     |     | |   | | ||   || || | |   ||| |||    ||  |||   | | ||||||| |||||||||||||||||||||||||| || |||||||||||||||||| | || | ||| ||||||| |||                          
--------gtaggccgcccgagacggaccaataatccccactccccata---tctaga---gtcttttac---ttaccaagcaaagcgctg---gaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA

upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATC----TGTTCGGAA---TGCAGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------
                   | |        || ||     |      |    | || |  ||| ||      || || |||  |  |||    ||||| |||   ||||||||||||| |||||||||||||| || || ||||| || || ||||||| | | || | ||  |||||||| ||                          
-------------------gtaacaaa-aactcttaaacccaattctacctctatgta-atgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA

upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTT--CGGAATGC---AGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------
                                            | ||   |  |     || | |   | |  |    | |  ||||   ||   |||  ||   |||| ||||||||||| ||||||||||||||||| || ||||| ||||||| || ||| | | | |||||||| ||                          
--------------------------------------------gtaacaatcat---cttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA

upper sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTT--CGGAATGC---AGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------
                                            | ||   |  |     || | |   | |  |    | |  ||||   ||   ||| |||   |||| ||||||||||| ||||||||||||||||| || ||||| ||||||| || ||| | | | |||||||| ||                          
--------------------------------------------gtaacaatcat---cttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA

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|67698812|gb|BJ959045.1|BJ959045
EST:     GATCGTTTGTCCGAGCTAGAGCCATTGGGTTGATGCCTATGATCGATCAG                         CAACGTGAGATCTGTTCGGAATGCAGGGTGAGAAGGACGACAAGATCATCG
genomic: GATCGTTTGTCCGAGCTAGAGCCATTGGGTTGATGCCTATGATCGATCAGgttagaagct ... tgcgggttagCAACGTGAGATCTGTTCGGAATGCAGGGTGAGAAGGACGACAAGATCATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTTCGGAATGCAGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA
                                      tgttttct  CT-rich tract