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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgatttatgcgcgaaatctcattgtcttgtatgcacaattttctcatatggtttctatatcttaaaactccgctctattacag

Basic information

species Arabidopsis thaliana
transcript AT4G05420.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 5'ss of exon 12
CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgt-ttgatttatgcgcgaaatctcattgtcttgtatgcacaattttctcatatggttt--ctatatcttaaaactccgctctattacag
||| || || ||||| || ||||||||||| |||||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||| |||||||| ||||| |||| ||| |  | |      ||||||   | |     | ||   ||||  |||   ||||||  |       |     ||||   
CCTTGACAGGCAGGGTCAGGGTCAGGTTGTCACTTGTTCAGGAGCATTTAAAGATGGTTCCCTTCGGGTGGTTCGGAATGGGATAGGTATCAATGAGCAGgtattgaattaagatctatccaatattgtccaatttt----agttctgcataaagttgagctatattatctcttatcatgtaattag--

upper sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 12
CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgatttatgcgcgaaatctcattgtcttgtatgcacaattttctcatatggtttctatatcttaaaactccgctctattacag
||| || || ||||| ||||||||||| || ||||||||||| || ||||| ||||||||||| || || ||||| ||||| ||||| || ||||| ||||| |  |||||| |     | | |||| |   | |  |   |       | | |  | ||| ||        | |||  ||||   
CCTTGATAGGCAGGGTCAAGGTCAGGTGGTCACTTGTTCTGGGGCGTTTAAAGATGGTTCCCTTCGGGTGGTTCGTAATGGTATAGGGATTAATGAGCAGgtatt-tttatg-gtagtttattattgccaactttttaatgtggagaagttttgagt-tatttccccctctcctgcttgattag--

upper sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA05G30530.1 (Glycine max), 5'ss of exon 12
CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgatttatgcgcgaaatctcattgt------cttgtatgcacaattttctcatatggtttctatatcttaaaa-ctccgctctattacag---------------------------------------------------
||| || || ||||| |||||||||||||||||||| |||||||| |  ||||||||||| || ||||| ||||| |||||||||||||| |||||||||||  | |       |   | | || |||       |||    ||  | |   ||| | ||  |  | ||   |||| |    || |||  ||                                                    
CCTTGAAAGGCAGGGCCAAGGTCAGGTTGTAACTTGCTCTGGAGCTTACAAGGATGGTTCTCTTCGCGTCGTTCGTAATGGAATAGGAATTAATGAACAGgtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatctttatatcaatggcacacaccttacaaaatattaatttttttatgcatgtatttggtctag

upper sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 12
CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgatttatgcgcgaaatctcattgt------cttgtatgcacaattttctcatatggtttctatatcttaaaact---ccgctctattacag-------------------------------------------------
|||||| || ||||| |||||||||||||||||||| |||||||| |  ||||||||||| || || || ||||| ||||||||||| || |||||||||||  | |       |   | |||| |||       ||| |  ||  |     ||| | ||  |  | ||   |||| |    |  | |||||  |                                                 
CCTCGAAAGGCAGGGCCAAGGTCAGGTTGTAACTTGCTCTGGAGCTTACAAGGATGGTTCTCTTCGTGTCGTTCGTAATGGAATAGGGATTAATGAACAGgtcagctccccttcctctacctcagtgtggaatatttgcacccaagacacattcaaaaggaatggaaattggaaaaataaatctttatattaatgacaaactccttacaaaatattaatttttttatgcatgtatttgatctag

upper sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 12
CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgatttatgcgcgaaatctcattgtcttgtatgcacaattttctcatatggtttctatat-cttaaaactccgctctattacag-------------------
||| ||||| || || |||||||||||||||||||| || || || | ||| |||||||| || ||| | ||||| |||||||||||||||||||||||||| ||  ||||       || |  || | |  | |  | |||||     |    ||| ||  | |||  ||    ||| |||||  |                   
CCTGGAGAGGCAAGGCCAAGGTCAGGTTGTAACTTGCTCAGGGGCTTATAAAGATGGTTCTCTTCGCATTGTTCGAAATGGAATAGGAATCAATGAACAGgtctggcttatttcaaccattttcttat-tgatctctagaatttgactttgccatttataagttcttctaaacttgct-tattaatgtgcatatgccatcacatag

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|116483005|gb|EG525597.1|EG525597
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
EST: gi|116382317|gb|EG424909.1|EG424909
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
EST: gi|116382314|gb|EG424906.1|EG424906
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAACGTGGTCGTTGAAATCTTCA
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
EST: gi|116382319|gb|EG424911.1|EG424911
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAACGTGGTCGTTGAAATCTTCA
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
EST: gi|125218137|gb|EL232220.1|EL232220
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCGATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTG
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTG
EST: gi|116456286|gb|EG498878.1|EG498878
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
EST: gi|116455522|gb|EG498114.1|EG498114
EST:     AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAG                         GCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA
genomic: AGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgattta ... tctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCGAGAGACAGGGGCAAGGTCAGGTTGTAACTTGTTCTGGAGCATTTAAGGATGGTTCCCTCCGCGTAGTTCGCAATGGAATAGGAATCAATGAACAGgtttgatttatgcgcgaaatctcattgtcttgtatgcacaattttctcatatggtttctatatcttaaaactccgctctattacag

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