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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagttgtcaccgacacattcaagctcttgtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA

Basic information

species Physcomitrella patens
transcript PP1S490_20V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os09g12570.1 (Oryza sativa), 3'ss of exon 2
ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagttgtcaccgacacat-tcaagctcttgtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA
  |  | ||| |         ||    |   |  | | | |||   | ||     | ||| | | || |          | |      ||   |    |||   || ||||||||||| ||||||    |||| |||||||| |||||||||||||| || ||||||||| ||||  | || |||||  | ||||| ||| 
-catgtttgacagtttgagagtccacctagctcctcttgtactgcttatataaaatattattaacttttactaagtgtctgtttcttcctcaatctggcagAGTGTCCATGAAGGTCGCATCTACCAGCTGAAGCTGTTCTGTGACAAGGACTACCCAGAGAAGCCACCATCTGTCCGGTTTCATTCAAGAATCAATATGT

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os12g41220.1 (Oryza sativa), 3'ss of exon 2
------------------ttacttgtgataaaccccatt-tcattgtttttgatt-tcgcactctg---tctaagttgtgttactgagttgtcaccgacacattcaagctcttg---tttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA
                  || |||    |    | |||  || |  | | | | | | ||  ||||   || | | | | ||  |||  | |    |     ||| | |  |||   |||  | || | || ||||| || || || |||  | |||| || |||||||||||||||||||| || | |||||||||||| | ||| || ||  | ||||||||||
gtaagttgtttgtttccattgcttactcttgtactcataatcttcatatgtaactgttgcgttctgagctcgacgctttcttgttgatatatatttggt---ttcgaacatttgaatttttgatagACTGTCCATGAGGGCCGGATATACCAACTGAAGCTTTTCTGCGACAAGGACTACCCAGACAGGCCACCAACTGTAAAATTTCACTCAAGAATCAACATGA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G056501_T02 (Zea mays), 3'ss of exon 2
ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagttgtcaccgacacat-tcaagctcttgtttg---tacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA
  ||   ||| |      | |        | |  ||||  ||  |   |   |||  |   | ||||     |||    | | || ||||| | |    |  || | || ||||| ||||| ||||||    ||||  |||||||||||||||||||||| || ||||||||| | ||| |||| |||||  | || ||| | |
-gacacttgaaatctttgactgatgaagctgtactttcctacatttctt---ttgcttatttcagtttatgtcgagttgtattaatctcttttcttacttgaagACCGTCCATGAGGGTCGCATCTACCAGCTGAAGTTGTTCTGCGACAAGGACTACCCTGAGAAGCCACCATCAGTTCGATTTCATTCAAGAATAAACTTAA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ15952 (Selaginella moellendorffii), 3'ss of exon 2
ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagt-tgtcaccgacacattcaagctcttgtt-tgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA
                    | |  | | |||  ||||   || ||         ||  ||||| | | || |       ||    |  || || ||| ||||| ||||| ||||| || || ||     | ||  ||| ||||||||| ||||| || ||||||||||||| |||  |||||||||| || ||||||||||
-------------------gtcctctttcttttttttctttctttgctcttacaatgc-actgactctttcgctttttttttttctcatttattctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ33318 (Selaginella moellendorffii), 3'ss of exon 2
ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagttgtcaccgacacattcaagctcttgtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA
                    | |  | | |||  ||||   || ||      |  ||   |||| |  |   |      |||    |  | | ||| ||||| ||||| ||||| || || ||   | | ||  ||| ||||||||| ||||| || ||||||||||||| |||  |||||||||| || ||||||||||
-------------------gtcctctttcttttttttctttctttgctcttataatgcc-ctgactctttcgcttttttttctcatttat-tctgtgcagTCTGTTCACGAAGGACGCATTTATCAACTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA

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|208365088|gb|DC947324.1|DC947324
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|37821329|gb|BJ579395.1|BJ579395
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162211664|gb|FC387952.1|FC387952
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|67573475|gb|BJ946299.1|BJ946299
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|100446255|gb|CJ970554.1|CJ970554
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162176507|gb|FC352976.1|FC352976
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|208388041|gb|DC941694.1|DC941694
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162248628|gb|FC424481.1|FC424481
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|67696855|gb|BJ957088.1|BJ957088
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|18348930|gb|BJ180979.1|BJ180979
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|15320319|gb|BI488125.1|BI488125
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|18355140|gb|BJ187199.1|BJ187199
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|100447101|gb|CJ971400.1|CJ971400
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162245980|gb|FC424378.1|FC424378
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|67575457|gb|BJ948281.1|BJ948281
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctaagttgtgttactgagttgtcaccgacacattcaagctcttgtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA
                                        ctcttgttt  CT-rich tract