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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctcccatttttcaaacatgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 8
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctcccatttttcaaacatgaccc-ttggtgataagtaaaa----ggctctcataacacaactaacccaactgaatgaatccag------------
||| || ||||| || || ||  | ||||| |||||||| || ||| ||||||||||||| || || ||| | |||||||| ||||| ||||||||||| ||  || ||    |  | | |    | | |   |  || | | | |       ||| |  |||  ||     |     | ||  |||                
TGCTGACATTCTTGATCCTGCTTTGATGCGATCTGGTCGTTTGGACCGAAAGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 7
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctcccattttt-caaacatgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag----------------
||| || || || ||||| || || ||||| ||||| || || ||| |||||||||||||||| |||||| |||||||||| ||||| ||||||||||| ||  |||||  | | || | |  | ||  |    | |  | |||      |     ||   ||  || | ||||| || |  | | |                
TGCTGACATCCTTGACCCTGCTCTGATGCGATCTGGACGGTTGGACCGAAAGATTGAGTTCCCTCACCCATCCGAAGAAGCAAGAGCTAGAATCTTGCAAgtcggtctcaacaacttatgctcaaattgctgaagtttgtcagtggctttcctcagtaggccatttatcacaact-aacgtgttctgtattggtcctctgtag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G100873_T01 (Zea mays), 5'ss of exon 1
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctcccattt---ttcaaaca--tgacccttggtgataagtaaaaggctctcataacacaactaacc------caactgaatgaatccag---------------
  | ||  | || ||||| || || ||||| || || ||  | ||| | |||||||||||||| |||||| | |||||||| ||||| ||||||||||| ||  |||||  | | ||   |||||     |||   |||   || | | |     |  | | || ||      |      ||||||| ||  | | |               
CACCGACGTCCTTGACCCTGCTCTGATGCGATCAGGACGGCTGGACCGCAAGATTGAGTTCCCTCACCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactga-tgttttctgtatgtcgcactgtag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 8
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctcccatttttcaaacatgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag
|||||||||||| ||||| || || ||||||||||||||||||||  | || |||||||| ||||||||||  |||||||| |||||  ||||  | ||||||||        |   ||||        | |   |   ||  | ||   |  |        |||   |  |||     | | |||
TGCAGATATTCTTGACCCTGCCCTTATGCGTTCTGGTCGATTAGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttggtgtctttaaacttcatctgctgacttgtttttcaaacagaacatttac------tgactgctctcactttgatatttcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 8
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttg-tctctcccatttttcaaacatgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag
||| || ||||| || || || || ||||||||||||||||| ||  |||| |||||||||||||||||||| |||||||| |||||  ||||  | |||||||| | ||| | | ||||      ||||  ||  |       | ||   |  | ||        |    ||    ||        
TGCTGACATTCTTGATCCTGCCCTTATGCGTTCTGGTCGATTGGATCGAAAAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAGgtttggtatcttcaaattttatttgctgacattttttctctgacagaacttttgcttatgtttttcacattaatatcatag------

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtc-tctcccatttttcaaaca-tgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag
|||||||||||| || || || || |||||||||||||| || ||  | || |||||||| ||||||||||  |||||||| |||||  ||||  | |||||||||  ||| |||   || |     |||| | | ||   ||  ||||   |  |        |||| ||  |||     | |  ||
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactttacctgctgacacattgtt-caatcaaaacatttac------tgactaccctcactttgatattttag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 8
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctccc--atttttcaaacatgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaat-gaatccag--
 || |||||||||||||| ||||| ||||| ||||||||||| ||  | || |||||||| ||||| || || |||||||| |||||  ||||||||||||| |||||       || |||    |  || | ||    ||   | |     |           | | || |      || | ||      
AGCTGATATTCTGGACCCTGCACTTATGCGATCTGGTCGATTGGATCGTAAAATTGAGTTTCCACATCCCACTGAAGAAGCAAGAGCTCGAATCTTGCAGgtatgtcttcaatgaatattttcttctagatcattacacattgatcactctttgcagagctcttattgactctttcacattgtatttgtag

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|164062577|gb|ES093452.1|ES093452
EST:     AGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAG                         ATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGC
genomic: AGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctct ... atgaatccagATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGC
EST: gi|124857255|gb|EH941692.1|EH941692
EST:     ACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAG                         ATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGCTT
genomic: ACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctct ... atgaatccagATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGCTT
EST: gi|124734772|gb|EH826174.1|EH826174
EST:     AGATTGAGTTCCCACGCCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAG                         ATTCACTCAAGGAAG
genomic: AGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctct ... atgaatccagATTCACTCAAGGAAG
EST: gi|164146057|gb|ES101754.1|ES101754
EST:     AGATTGAGTTCCCANACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAG                         ATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGC
genomic: AGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctct ... atgaatccagATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtctctcccatttttcaaacatgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA