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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_20V6.1
intron # 3
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|162211664|gb|FC387952.1|FC387952
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|18348930|gb|BJ180979.1|BJ180979
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162248628|gb|FC424481.1|FC424481
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|67573475|gb|BJ946299.1|BJ946299
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162176507|gb|FC352976.1|FC352976
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|67696855|gb|BJ957088.1|BJ957088
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|100447101|gb|CJ971400.1|CJ971400
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|37821329|gb|BJ579395.1|BJ579395
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|15320319|gb|BI488125.1|BI488125
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|208388041|gb|DC941694.1|DC941694
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|18353181|gb|BJ185236.1|BJ185236
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|100446255|gb|CJ970554.1|CJ970554
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|100440583|gb|BY962270.1|BY962270
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|208388103|gb|DC933181.1|DC933181
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|162245980|gb|FC424378.1|FC424378
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|18355140|gb|BJ187199.1|BJ187199
EST:     ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCAC                         TCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
genomic: ATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagttccg ... gtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGAC
EST: gi|18372883|gb|BJ204485.1|BJ204485
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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagttgtcaccgacacattcaagctcttgtttgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacattc