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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag

Basic information

species Arabidopsis thaliana
transcript AT3G13470.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 12
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag
|||||||| |||||||| |  ||||| ||||| ||||| || |||||||| |||||||||||||||||||||||||| ||||| | ||||||||||| | |    | |  | |   |   | ||           |  |  | | |  | |||||     | |||    |      
GTTGGAGCTGAAATTGTAAGGAGAGCGCTGAGCTACCCGCTTAAATTGATTGCTAAGAATGCTGGTGTTAATGGAAGCGTTGTTACCGAGAAGgttagatcttgttcacta-acagaaaatcatatgttcacatgtacatctgaataacataaaagatgatgttttaccag-----

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 12
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgtt---ataacaacataagaacat-----ccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttat-ttattgcag
||||| || ||||| || |  |   |  |||||||||| || ||||| ||||| || |||||||||||||| || |||||||| |  |||||||||   |     ||||  |  | |     | |||  ||| ||  |||  | || |||  ||  |   ||    || |  | | | ||| |||
GTTGGGGCTGAAATCGTAAGGAAGTCCTTGAGTTACCCACTTAAATTAATAGCAAAAAATGCTGGTGTTAACGGCAGTGTTGTTACTGAGAAGgtttgtactctgacatttgttcttaagtacgatgaatatgcaattctgcagct-cgtgtgtaac--gaatttttgaacatgtatgatttcag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 11
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag----
|||||||| || ||||| |||||||| || ||||||||| ||||||| || || |||||||||||||| ||||| ||||||||||| |||||||| || |     ||      || |||   | |      ||  ||||||   || | ||   | | |||   | | | ||| |     
GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGgt-atcaaggtttag-----tctatgtagaatttctcttttctctacgagcgtgg-ttgtgatgatgtgact-tgtgttgtaattag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G18760.3 (Glycine max), 5'ss of exon 11
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag----
       | || ||||| |||||||| || ||||||||| ||||||| || || |||||||||||||| ||||| ||||||||||| |||||||| || |     ||      || |||   | |      ||  ||||||   || | ||   | | |||   | | | ||| |     
-------CTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGgt-atcaaggtttag-----tctatgtagaatttctcttttctctacgagcgtgg-ttgtgatgatgtgact-tgtgttgtaattag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 11
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag----
|||||||| || ||||| |||||||| || ||||||||| ||||||| || || || || |||||||| ||||| ||||||||||| ||||||||  |||     |  |  |||  |   ||  ||   |||    ||||| | || | ||   | | |||   | | |  ||  |    
GTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAAAACGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGgtactaaggt--ttggtccatttagaatttctcttttct----ctacgaatgtgg-ttgtgatgatgtgact-tgtgctgtggttag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 12
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacata-----agaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag
|||||||| || ||||| || |||||  |||||||||||||||| || || || || ||||||||||||||||||||||| ||||| ||||||||   | |||         || |  |||||| |  |     || |||| ||  |  ||||   |||  |  |   || || |      
GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATTGCCAAAAATGCTGGTGTTAATGGAAGTGTGGTCAGTGAGAAGgtataatcaatgagtttccaggaggtccatgatc-tctgtttcatgatgtatatgtgttgaccaaatgg--gagctttttcag-----

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag------------------------------------------------------
||||| || || ||||| |   | ||  || |||||||| |||||||||| || |||||||||||||| || ||||| || ||    |||||||||    |    | ||  ||    |     ||   ||    |  | |    | || |   |    | ||| ||   |||   |                                                      
GTTGGCGCTGAGATTGTGAGGCGGGCCTTGTGTTACCCTTTGAAATTGATCGCCAAGAATGCTGGTGTGAACGGAAGCGTGGTGGTTGAGAAGgttggtgc---cttagtgcactgttttagttttgactgcaaacatgcacgtggtgataggatttgtatatctaaccatttaggatgtggcaacgggaagtctggtcgtttaatcagttgaggttacgtgctcatcag

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|19878666|gb|AU239497.1|AU239497
EST:     ATTGATAGCTAAGAATGCNTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG                         GTGCTGGCTAACGATAATGTGAAATTTGGATACAATGCTGCAACCGGCAAG
genomic: ATTGATAGCTAAGAATGC-TGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaa ... tttattgcagGTGCTGGCTAACGATAATGTGAAATTTGGATACAATGCTGCAACCGGCAAG
EST: gi|164117296|gb|EL983008.1|EL983008
EST:     AATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG                         GTGCTGGCTAACGATAATGTGAAATTTGGATACAATGC
genomic: AATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaa ... tttattgcagGTGCTGGCTAACGATAATGTGAAATTTGGATACAATGC
EST: gi|125208624|gb|EL223578.1|EL223578
EST:     AATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG                         GTGCTGGCTAACGATAA
genomic: AATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaa ... tttattgcagGTGCTGGCTAACGATAA
EST: gi|124909331|gb|EH983411.1|EH983411
EST:     ATTGATAGCTAAGAATGTCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAG                         GTGCTGGCTAACG
genomic: ATTGATAGCTAAGAATG-CTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaa ... tttattgcagGTGCTGGCTAACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATAGCTAAGAATGCTGGTGTTAATGGAAGTGTTGTCAGCGAGAAGgttataacaacataagaacatccatgcttattcagctcttgatctacgtaagttgcttaaaaagctgtatttatttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG