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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaag

Basic information

species Arabidopsis thaliana
transcript AT1G55490.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 5'ss of exon 9
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcct--ttgtctgattaagatgtgtttcagagatattaagtt---aagctcgttatgtattggttaaag---------------------------------
   || || ||||| ||||||||||| || ||||||||||| |||||||||||  ||||||| ||||| || ||||||||| | ||| || |    ||  | ||   || ||||  |  | | | ||||   | | ||   ||   ||| | | ||  | | |||||                                    
GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAGCTTGCTGGTGGTGTTGCAGTCATTCAGgtataataagaaatggacaaaatgccatgttatctgtatctgttctttttcttggttctttgtttggaaagatagatagatgt-ggttatgtgggtcgtaatccaagttttgttacttttgatag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 9
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagttt-cctttgt-ctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaag---------------
   || || || || || ||||| || ||||| ||||||||||| || |||||||||||||| |||||||| || ||||| | ||  |   | |  || |   ||  ||  ||  ||||  |     |  |    |||     ||| |  || | | |    | | |               
GTTGCTGAACAGGAATATGAGAAAGAAAAACTGAATGAGAGAATAGCTAAGCTCTCTGGTGGTGTTGCTGTCATCCAGgtgatctcgatgttctgcaattgaaccaatgcacttgttaatgtactactaggctgcatttgcagaagataattgt-tgtgaaatgacgctacttgttatgtag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 3
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgta-----aactaaaaactatttaagtttcct-ttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaag-----------------------
  ||| || ||||| || || ||||| || ||||||||||| || ||||||||  ||||||| |||||||| |||||||||     || || | |      || |||  | || | || |  |  |   || ||  |||   | |||       |  || ||   |  |||                       
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 9
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaact---atttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaag-----------------------------------
    | || ||||| || ||||  || ||||| || ||||| || || || ||||||||||| |||||||| ||||||||||||   ||  |   |    |||| |||   | |    ||    |  ||      |  |   || ||   | |  | |      |||                                    
GCTACTGAACAAGAATATGAGAGAGAAAAACTAAACGAGAGGATAGCTAAACTCTCTGGTGGTGTTGCTGTCATTCAGgtaaaccccaatgttaaaccctagttgcctcaatttttcaaaaccttagttgcctcttggtgtatttaggatgcttagcagaataaaaaaaactagaacatgatatgccttgctttgtattgtag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 9
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagt-taagctcgttatgtattgg----ttaaag
  ||| |||||||| || |||||||| ||||| ||||| |||||||||||  | || ||||| |||||||||||||||||||| |   |  || |  ||||    || | | | | |  |     |   || |  | ||| |    |  ||||  ||||     || |||
GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattcttagttagtccagttaaaatt-tataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 6
----------------------CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaa-gctcgttatgtattggttaaag-----------------------------------------------------------
                         || |||||||| |||||||||||||| || |||||||||||||| ||| | || || || || ||  | ||||||||| |       ||   |  |||||  |  |   || |  || ||||       | |   |  |  |  |  ||| ||||  | |||                                                            
CCAAATTCGCAACCTTATCGAAATTGCTGAGCAAGAGTACGAGAAGGAGAAGCTGAATGAGAGAATTGCGAAGTTATCGGGAGGTGTCGCCATTATTCAGgtatat----gtcttcatttgtttcaatcat--aataagaatctgttagctccctgtcgtgacagcgtccactatatattc-tcaaattgttccgtgttgtggtttgcacaatgaaggcctctcttgacgtgggacttcctgcgcag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 5'ss of exon 6
----------------------CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcct---ttgtctgattaagatgtgt-ttcagagatattaagt-taagctcgttatgtat-tggttaaag------------------------------------------------------------------------------------------------------
                         || |||||||| || ||||||||||| || |||||||| ||||| ||||| ||||| ||||| ||  | |||||||||   |   |  ||  | |  |   |   | ||| | ||||    | | ||  || || |||      | ||   |||  |  | ||  |                                                                                                        
CCAAATCCGCAACCTAATCGAAGTCGCCGAGCAAGAGTATGAGAAGGAGAAGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttcttatttacattaactctttggctcgtcgggttaacgaatctcttttgatatgttatacacgaactatatattcaccttgtcgattctattttaagcatacctaaatgtgattaggctcttctttcgttgaccgtggtaaaatgatgtggaagataaatcttcggtaagtcgtaactgttatttgcag

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|125224063|gb|EL238148.1|EL238148
EST:     AGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAA
genomic: AGTTGCTGTGATTCAGgtaaactaaa ... ttggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAA
EST: gi|47832210|gb|CK121894.1|CK121894
EST:     AACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAACTCAA
genomic: AACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaa ... ttggttaaagGTTGGAGCACAAACTGAGACAGAACTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaag

- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG