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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcagcttaagtgattgaagctccactttatttctttatgattatgatcctcacgcctttgccgtattgaaattccgtaactttgtacctcaata...

Basic information

species Physcomitrella patens
transcript PP1S301_53V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcagcttaagtgattgaagctccactttatttctttatgattatgatcctcacgcctttgccgtattgaaattccgtaac-tttgtacctcaata------
||||||||||||||||||||| || || |||||||||||||| || |||  | | |  | ||| || ||||||||||| ||||| || ||||  |||||||||     |    || |   | | |  |||       | || | ||||    ||  || |||  |  | |  | |  |   ||||| |||   |||   |       
GGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggagaa---aaatatgttaggacccaggaatggttttcaagatt----tctgcatgccaatatctttctaatctaatgtaacatttaagcctgtcttgaccaa

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcagcttaagtgattgaagctccactttatttctttatgattatgatcc-tcacgcctttgccgtattgaaattccgtaactttgtacctcaata-----------
||| || || ||||| ||||| ||||| || |||||||| || ||||||| ||| | |||||| |||||||||||||| ||||| || ||||| |||||||||        | || ||| |||    |      || | || |    | | ||   |||   | |||    ||||    | |  || |||| || ||               
GGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATAAAACGATCAAATTTTGGAAGgta--------tgaaatgaatgatcacctttagcatgttttcagtgctgtcatttatcaattcattgataaattg----tgcacaagtttgcacttctgaggaactaagttt

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcagcttaagtgattgaagctccactttatttctttatgattatgatcctcacgcctttgccgtat-tgaaattccgtaactttgtacctcaata-
|||||| || ||||| ||||| ||||| || |||||||| |  ||||||| ||| |  ||||| |||||||||||||| ||||| || ||||| |||||||||      |  | |     |  |||     |||| | || |    |||| |   |||    |     ||     |  || |    ||  | | || | |  
GGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATAAAACAATCAAATTTTGGAAGgtatgaaatgaatgatcacctttagcatgcttttagtgctgt-catttatcaat-tcattgataaattgtgcacaaggttgcacttctgaggaactaagttt

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcag--------cttaagtga--ttgaagctcc--acttt--atttctttat-gattatgatcctcacgcctttgccgtattgaaattccgtaactttgtacctcaata--------------------------------------------------
||||||||||||||| |||||||| || || ||||||||||| || |||| ||| | ||| || || ||||| ||||| ||||| ||||| || |||||||||      |        |||| |  |  || ||  |||  | |||  |||| || |  ||||||| ||  ||   |     |   ||    |||  |||||    |  | ||||                                                  
GGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATAAAACCATTAAGTTTTGGAAGgtaggaagggaaaattgtcttatgaaactttaaacttcctgatttttaatttgttgacagattatgctcaacatcaccaactccagtttggtttctttaactactgatat-aatatatatcctgcacatgctgattacatagctgtcttttcgagaatgaaacag

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|100404937|gb|BY991356.1|BY991356
EST:     TGCTCAGTTCCTACTTTCTACAAATGANCAAA-CTATTAAATTGTGGAAG                         GTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGGATCTGG
genomic: TGCTCAGTTCCTACTTTCTACAAATGA-CAAAACTATTAAATTGTGGAAGgtactcgcag ... aatactgcagGTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGAATCTGG
EST: gi|100446612|gb|CJ970911.1|CJ970911
EST:     CTGCTCANTTCCTACTTTCTACAAATGACAAA-CTATTAAATNGTGGAAG                         GTGACTGAAA-GAA-CTGAA-CA-GTGAAAA-TCTGA-TCTGGAT-CTGGA
genomic: CTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcag ... aatactgcagGTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGAATCTGGATTCTGGA
EST: gi|162155365|gb|FC331979.1|FC331979
EST:     CTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAG                         GTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGAATCTGGATTCTGGA
genomic: CTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcag ... aatactgcagGTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGAATCTGGATTCTGGA
EST: gi|162152096|gb|FC328686.1|FC328686
EST:     CTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAG                         GTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGAATCTGGATTCTGGA
genomic: CTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcag ... aatactgcagGTGACTGAAAAGAAACTGAAACAAGTGAAGAGTCTGAATCTGGATTCTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACAAAACTATTAAATTGTGGAAGgtactcgcagcttaagtgattgaagctccactttatttctttatgattatgatcctcacgcctttgccgtattgaaattccgtaactttgtacctcaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG