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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGAAAGCATGCATCCATCCATCCTTGCAGGCATGGTGCAGTTATGAAGAAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccctgcattcctgctcttagaaatgtgctaaggatgaaacgtagttctattccatattttttctacttcatattgcactgttgaattttttct...

Basic information

species Physcomitrella patens
transcript PP1S62_116V6.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_116V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA12G00830.5 (Glycine max), 5'ss of exon 7
CAGGAAAGCATGCATCCATCCATCCTTGCAGGCATGGTGCAGTTATGAAGAAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccctgcattcctgctcttagaaatgtgctaaggatgaaacgtagttctattccatattttttctacttcatattgcactgttg-aattttttct--
|||| ||||||||||| || ||||| ||  | ||||| ||||| |||||||||||||||||  |  |  | || || || ||| | |||||||| ||||||||  ||||||   |||||  |  ||    | |  |  |||  ||   |   || ||   ||||   ||    ||    |||    |||   | |  |  |  
CAGGGAAGCATGCATCTATTCATCCATGTCGACATGGAGCAGTGATGAAGAAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgta--aaccctttcttccta-tgatattgctttcatttggagaaacaattcatccatatgatataaattgaggttgtctttgattagttatgactactggtaa

upper sequence: PP1S62_116V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA09G36540.1 (Glycine max), 5'ss of exon 8
CAGGAAAGCATGCATCCATCCATCCTTGCAGGCATGGTGCAGTTATGAAGAAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccctgcattcctgctcttagaaatgtgctaaggatgaaacgtagttctattccatattttttcta-cttcatattgcactgttgaattttttct-------
|||| ||||||||||| || ||||| ||  | ||||| ||||| |||||||||||||||||  |  |  | || |  || ||| | |||||||| ||||||||  ||||||   |||||      ||| || ||||    ||   |   | |  |  | |||||  | |  | |  |||  |    || | | ||   | |       
CAGGGAAGCATGCATCTATTCATCCATGTCGACATGGAGCAGTGATGAAGAAAATCATTGATGTGTTGATGTCACACGGAGTTGAGCCTGAAGTTGACAAgta--aaccctttcttccta-----agatat-tgctttcaattggagaaactattcattcatatgatataaatcgacatggtcttttgattagttcaatatgactacc
















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|208382587|gb|DC923215.1|DC923215
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|37850632|gb|BJ608640.1|BJ608640
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|208393991|gb|DC928743.1|DC928743
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|37825564|gb|BJ583630.1|BJ583630
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|18334041|gb|BJ166057.1|BJ166057
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|162174528|gb|FC350183.1|FC350183
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|162164442|gb|FC341568.1|FC341568
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|162165647|gb|FC341486.1|FC341486
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
EST: gi|208396622|gb|DC920358.1|DC920358
EST:     AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAA                         ATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA
genomic: AAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccc ... tgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGAAAGCATGCATCCATCCATCCTTGCAGGCATGGTGCAGTTATGAAGAAAATCATTGACATACTCCTTTCCCGTGGTGTTAATCCTGAAGTAGACAAgtatgaaccctgcattcctgctcttagaaatgtgctaaggatgaaacgtagttctattccatattttttctacttcatattgcactgttgaattttttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG