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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccag

Basic information

species Arabidopsis thaliana
transcript AT1G79000.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 9
AGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaa--tgatcaagg--cgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccag
|||||||||||| || ||||||||||||||||| ||||| || ||| | ||||||||||  || ||||  ||||| ||||| ||  |||||||||||||||||||||  |  || ||     | |       ||   | | | | ||   ||   | ||   |  | |  |  | |    ||| | |    |                            
AGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACTACCCGACAGAGTTCCCATACAAGTCCAAGgtaagaaattagtccagtattctttcaaaagaacaccaatcatttcaagcataaatcatacgt--gaaactgttttttatcaaatgtttggcag--------------------------

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G139977_T02 (Zea mays), 5'ss of exon 2
AGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccag
|||||||||||| || || ||||||||||| || ||||| || ||| | ||||||||||  || || |  ||||| ||||| ||  | ||||||||||||||||||||           ||| |||| | |  |   |     | ||  |   | |     | | |   |   | |    |||  || | |       | ||              
AGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaatt---------cattcttgtcatttgaagcatgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacag-------------

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA07G00230.1 (Glycine max), 5'ss of exon 9
AGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccag
|||||| |||||||||||||| ||| | ||||| ||||| || ||||| || ||||||| ||| || | |||||||||||||||| |||| || || ||||| |   ||   |||     ||| | |||        | || |   |    | |||  ||  || | | | |  | |  ||| | |||| | |||                     
AGTTGTGTCATCTGTTGACAAAAAGTTAGAAGTGAAACCGCGGTTTCTGGAGATTTTTCAGGAAGAGAATTACCCAACAGAATTTCCATATAAATCAAAGgtga---tgggaaag-----ttgattttatccatccgattgtaatcaaa--tcattaatcatgaatacttttgattcccttagctttct-attccag-------------------

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA08G24290.1 (Glycine max), 5'ss of exon 11
AGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccag
|||||| |||||||||||||| ||| | ||||| ||||| || ||||| || ||||||| ||| || | |||||||||||||||| |||| || || ||||| |  |  |    |   |||   | | |  |||   |  | ||     | ||| |  |  | |  |  | |  | |  ||| | |||| | |||                     
AGTTGTGTCATCTGTTGACAAAAAGTTAGAAGTGAAACCGCGGTTTCTGGAGATTTTTCAGGAAGAGAATTACCCAACAGAATTTCCATATAAATCAAAGgtgatgagaaagttgatttatcaatctgatcgta---atcgaat-----cattaatcat--gaatattatttgatgcccttagctttct-attccag-------------------

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|116465026|gb|EG507618.1|EG507618
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAG-CGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116428303|gb|EG470895.1|EG470895
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116462330|gb|EG504922.1|EG504922
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116447334|gb|EG489926.1|EG489926
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116414729|gb|EG457321.1|EG457321
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGAT
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGAT
EST: gi|116455250|gb|EG497842.1|EG497842
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116455249|gb|EG497841.1|EG497841
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116418401|gb|EG460993.1|EG460993
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116447332|gb|EG489924.1|EG489924
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT