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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACACTTGTGAGGACTCTCTCTTGGCTGCACCAATTATCTTGGATCTTGTCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattccgttagttagttaccaagaaactcgagattggtgagtttttttttttcatgtttgaatctattctctttcag

Basic information

species Arabidopsis thaliana
transcript AT2G22240.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G02210.3 (Glycine max), 5'ss of exon 8
TAACACTTGTGAGGACTCTCTCTTGGCTGCACCAATTATCTTGGATCTTGTCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattccgttagttagttaccaagaaactcga---gattggtgagtttttttttttca--tgtttgaatctattctctttcag------------
 ||||| |||||||| || || || ||||| || |||||||||||  | |||||||| ||||| || ||||| |||||||| ||||||||||||   ||||| || || |  ||  | | | |        || ||    ||| || | | | |||||||||    | |||    | | | ||   |            
CAACACATGTGAGGATTCCCTTTTAGCTGCTCCTATTATCTTGGACTTGGTCCTTCTTGCTGAGCTGAGCACTAGAATCCAGTTTAAAGCTGAAAATGAGgtctgcatgc-attgctaaatgattttattgcttgattgtattcgtcattgtatttttttcagccttctgaggtcactatgttgtggtggttgatgcag

upper sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G14670.2 (Glycine max), 5'ss of exon 8
TAACACTTGTGAGGACTCTCTCTTGGCTGCACCAATTATCTTGGATCTTGTCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattccgttagttagttaccaag--aaactcgagattggtgagtttttttttttcatgtttgaatctattctct---ttcag---
 |||||||||||||| || || || ||||| || |||||||||||  | |||||||| ||||| || |||||  ||||| | ||||||||||||   ||||||||   |  |||  |||   |   |    |||      ||  |   |||  |||||| | |  | ||   | | | |   || |    
CAACACTTGTGAGGATTCACTGTTAGCTGCTCCTATTATCTTGGACTTGGTCCTTCTTGCTGAGCTTAGCACTCGAATCGAGTTTAAAGCTGAAAATGAGgtttgccatatgttgcttaaccattcattccaacctctatttcttatctttagttttttaaagactcaaatgagtttatggctttaacag

upper sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G31450.4 (Glycine max), 5'ss of exon 5
TAACACTTGTGAGGACTCTCTCTTGGCTGCACCAATTATCTTGGATCTTGTCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattccgttagttagttaccaagaaactcgag-----attggtgagtttt--tttttttcatgtttgaatctattctc--tttcag---
 ||||| |||||||| || || || ||||| || |||||||||||  | |||||||| ||||| ||||||||  ||||| | ||||||||||||   |||||||||  |   |  |||  |||   |   | || |      ||   | | ||||  ||||||  |   |  |||   ||      ||||    
CAACACATGTGAGGATTCACTGTTAGCTGCTCCTATTATCTTGGACTTGGTCCTTCTTGCTGAGCTCAGCACTCGAATCGAGTTTAAAGCTGAAAATGAGgtttgtcatatatatgttgcttaatcattcattccaagctctatctcttatttttagttttttaaagactcaaatgagtttatggcttcaacag

upper sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 5'ss of exon 8
TAACACTTGTGAGGACTCTCTCTTGGCTGCACCAATTATCTTGGATCTTGTCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattccgttagttagttaccaagaaactcgagattggtgagtttttttttttcatgtttgaatctattctct-ttcag--------
 ||||| || |||||||| ||||| ||||| || || ||||||||| | |||||||| ||||| ||||||||| | |||||  | ||||||||||||||||| ||| |||   |   |  |||    ||  |||  | ||  ||  ||||    |  ||||     ||  ||    | ||||         
CAACACCTGCGAGGACTCACTCTTAGCTGCTCCCATCATCTTGGATTTGGTCCTTCTTGCTGAGCTCAGCACCCGCATCCAGCTCAAAGCTGAAGGAGAGgtctgttttcttctgcatccttat-gggaccctcttgctt--tggtttttaccatcacatggaatgattcataggatgttcaattttgcag

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|164125201|gb|ES085999.1|ES085999
EST:     TCCTTCTCGCTGAACTCAGCACCAGAATCCAGTTTAAAGCTGAAGGAGAG                         GGGAA-TTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTC
genomic: TCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattc ... tctctttcagGGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTC
EST: gi|164014546|gb|ES157540.1|ES157540
EST:     CTCGCTGAACTCAGCACCAGAATCCAGTTTAAAGCTGAAGGAGAG                         GGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCACA
genomic: CTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattc ... tctctttcagGGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCACA
EST: gi|164206078|gb|ES170613.1|ES170613
EST:     CTCGCTGAACTCAGCACCTAGAATCCAGTTTAAAGCTGAAGGAGAG                         GGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCACA
genomic: CTCGCTGAACTCAGCACC-AGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattc ... tctctttcagGGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCACA
EST: gi|164122078|gb|EL987080.1|EL987080
EST:     CTGAAGGAGAG                         GGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCACA
genomic: CTGAAGGAGAGgtttgtattc ... tctctttcagGGGAAGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCACA
EST: gi|164228430|gb|EL989803.1|EL989803
EST:     CTGAAGGAGAG                         GGGAAGGTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCAC
genomic: CTGAAGGAGAGgtttgtattc ... tctctttcagGGGAA-GTTTCACTCTTTCCACCCGGTAGCTACCATACTCAGTTACCTCAC
EST: gi|164008166|gb|ES028634.1|ES028634
EST:     TCCTTCTCGCTGAACTCAGCACCAGAATCCAGTTTAAAGCTGAAGGAGAG                         GGGAAGTTTCACTCTTTCCACCCGG
genomic: TCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattc ... tctctttcagGGGAAGTTTCACTCTTTCCACCCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACACTTGTGAGGACTCTCTCTTGGCTGCACCAATTATCTTGGATCTTGTCCTTCTCGCTGAACTCAGCACCAGAATCCAATTTAAAGCTGAAGGAGAGgtttgtattccgttagttagttaccaagaaactcgagattggtgagtttttttttttcatgtttgaatctattctctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA