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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G18710.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttc--------agtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatc-----atgttcttatg-cag
 || ||||| || ||||||||||||||||| || ||||| |||||||| ||||| || ||||| ||||| || |||||||| ||| | |||||||||||||| |   | | | ||        || |||      |||||   ||| ||  || |||    |  |   | ||| ||| |||||      ||||   | || |||
TTATCGTGCTCCTGAGCTCATATTTGGTGCAACCGAGTATACAACTTCAATTGACATATGGTCAGCTGGATGCGTTCTTGCAGAGTTACTTCTTGGTCAGgttagtcactatatctttatctaaggaactgcaacattcaggttccttgattagattatgctgtgatgttattctgattatatttcataatgtgtatttgtcag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaa-ttctttcagtaaccagcttatt--caatctccatgtgta--tattt--gcattaggac-tcattgtgactat-atcatg-ttcttatgcag-------------
|||||| ||||| ||||||||||||||||| ||||| || || || || || ||||| ||||| ||||| ||||||||||| ||||| || |||||||||||       || ||||  |      |  ||   ||| ||    || ||  |||||  |||| | | | ||| |||  || | ||  || || |  || |              
CTACCGAGCACCGGAGCTCATATTTGGTGCAACTGAATATACTACATCAATAGATATATGGTCAGCTGGGTGTGTTCTTGCAGAGCTACTCCTTGGTCAGgttggtttcttttttctatggttgacagatctgcaaacttttggtttagttatttaagcatgatgtcatcactgttgctgtgattttgattatcttgtatttgtttttgctag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G472625_T02 (Zea mays), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaaca--attctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcat----tgtgactatatcatgttcttatgcag---------------
 || ||||| || |||||||||||||| || || ||||| |||||||| || || || ||||| ||||| |||||||| |||||| | ||||||||||||||       |||| |  | | |  | | || |  || |   |   |  ||||| |  |   |   |    ||||| | || | | ||    |   |               
TTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATATGGTCAGCTGGCTGTGTTCTAGCTGAGTTGCTTCTTGGTCAGgttggttgcattcatataatgattaacctaat--atttttgtacctcgatttg-accaaatcatgtatggtgtgattctaacctcttggggtcttggatcttatgtatcag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag
||| ||||| || ||||||||||||||||| || ||||| |||| ||| || || || ||||| |||||||||||||| |||||| | |||||||| |||||      | | ||||   |     | |   ||| |     |||||  |   |||   ||   |||     || |  |||   ||| |||
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt--tgccttcatataatgattcacctaatata---atgtatgatgtgattctaacctcttgg----atcttgtgtatgtat-cag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G43620.2 (Glycine max), 5'ss of exon 6
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgt--tcttatgcag-------------------
|||||| ||||| || || || ||||||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||||| ||| | ||||||||  |   || || |  |       ||||| ||      |   ||   |   ||||     || | | |||   |  ||   ||| |  ||                    
CTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTGCTTTTGGGTCAGgtttatg-ttattgcttttcttttgttattaaaatggtgtaaatagtctcatattaaataacaattt-actgcctagtgccatctgacacacaaatggaatttttttaaag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgta------aacaatt--ctttcagtaaccagc-ttatt-caatctccatgtgtatatttgcattaggactcattgtgactatatcat--gttcttatgcag-----------------------------------
||| ||||| || || || |||||||||||||| ||||| |||| ||| |||||||| ||||| ||||| ||||| ||||||||||||||| | || |||||       |   |||   ||||| |||  |   ||||| | || | |   | |||   |  | |   |      || | | |    |   || || | ||                                    
CTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTTCTTTTGGGCCAGgtttgtgtcattgatttgttttcattaattattattattactatgtactattatatgaatctactgcaaaatgaagtaaatgttctcttaattattttccacccatgtgttatctgaaataatttaaacttttgcag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G29200.1 (Glycine max), 5'ss of exon 6
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgt--tcttatgcag-------------------
|||||| ||||| || || || ||||||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||||| ||| | || |||||  |   || || |  |       ||||| ||      |   ||   |   ||||     || | | |||   |  ||   ||| |  ||                    
CTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTGCTTTTGGGCCAGgtttatg-ttattgcttttcttttgttattaaaatggtgtaaatagtctcatattaaataacaattt-actgcctagtgccatctgacacacaaatggaatttttttaaag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaa--------ttctttcagta----accagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag---------------
||| || ||||| || || || ||||||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||||| ||| | || |||||  |           |||||| | |     |   |   |   | ||||  | |  ||| ||   |    | | | ||     ||   ||  |   |  ||                
CTATCGGGCACCGGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTGCTTTTGGGCCAGgtttatgtcattgcttttcttttattgttagaatggtgcaaatagtctcattttcaataattatttagttatttactgcctacatgctat-ctgacacacaaatggaatttttgaag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA04G06760.1 (Glycine max), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaaca--------attctttcagtaacca--gcttattcaatctccatgtgtatatttgcattaggac----------tcattgtgactatatcatgttcttatgcag-------------------------
||| || ||||| || ||||||||||| ||||| ||||| |||| ||| |||||||| ||||| ||||| ||||| |||||||| |||||| | || |||||              |  ||||| |||  |  | |  | ||||     | | || |||| |   |  |           |  |  ||| ||| |      | | ||                            
CTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAACTTCTTTTGGGCCAGgtttgtgtcattgatgtgttttcattaattattgttactacaattctattatataaattttccacaaaatgatgtaaatgttctgttgattatctggcacccatgtgttatctaaaacaaattgaacttttgcag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G06850.1 (Glycine max), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgta------aacaatt--ctttcagtaaccagc-ttattcaatctccatgt-gtatatttgcattaggactcattgtgactatat-catgttcttatgcag------------------------------------
||| || ||||| || || |||||||| ||||| ||||| || | ||| |||||||| ||||| ||||| |||||||||||||| |||||| | || |||||       |   |||   ||||| |||  |   ||| |  |   | || | |||||  |     | ||  || ||| | | | | | || |  |||||                                      
CTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTTGGTCAGCTGGCTGTGTTCTTGCTGAACTTCTTTTGGGCCAGgtttgtgtcattgatttgttttcattaattattgttactacaatactatattgtataaattttccacgaaacaatgtaaatgttttcttgattatatgccacccatgtgttatctaaaacaatctaaactttttcag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 7
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcat-taggactca---ttgtgactatatcatgttcttatgcag---------------
|||||| ||||| || ||||||||||| ||||| ||||| ||||| || |||||||| ||||| ||||||||||| || |||||||||||||| || ||||| |||||||    ||| ||    |   ||    ||   ||   |||| || |  |  |  | |    |||||  | |   ||||| | ||                  
CTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATATGGTCAGCTGGTTGTGTCCTAGCTGAGCTTCTTCTAGGCCAGgtgaacaatttgcacagcaattttcagttttgcactttctgccaatatctggaaatgtgttttagttctgtgataaaactttgttcatttgacttattttcggttacag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 8
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag
 |||||||| || || || ||||||||||| ||||| ||||||||  | || || ||||||||  |||| || ||||| |||||| | ||||||||||||||     |     ||  |   || ||  | ||      |||    |    |  | |  | |||||   ||| |                 
TTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCTGGTCGACTGGATGCGTTCTGGCTGAGTTACTTCTTGGTCAGgttgtatacctcgtccttg--caactcttcca----ttatgccactcaccgtctcatcaatcatttccactgtgcag-------------

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 8
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag
||||||||| || || || ||||||||||| ||||| ||||||||  | || || ||||||||  |||| || ||||| |||||| | ||||||||||||||     |     ||  |   || ||  | ||      |||    |    |  | |  | |||||   ||| |                 
CTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCTGGTCGACTGGATGCGTTCTGGCTGAGTTACTTCTTGGTCAGgttgtatacctcgtccttg--caactcttcca----ttatgccactcaccgtctcatcaatcatttccactgtgcag-------------

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|124742043|gb|EH833205.1|EH833205
EST:     CTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
genomic: CTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
EST: gi|124913441|gb|EH987315.1|EH987315
EST:     TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAA
genomic: TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAA
EST: gi|164115188|gb|ES146159.1|ES146159
EST:     TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAATGCTGTGGATC
genomic: TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAATGCTGTGGATC
EST: gi|116451981|gb|EG494573.1|EG494573
EST:     TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
genomic: TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
EST: gi|124852165|gb|EH936602.1|EH936602
EST:     TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAATAGCTGTGGATCAGCTCGTTGAAAT
genomic: TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAAT-GCTGTGGATCAGCTCGTTGAAAT
EST: gi|116452048|gb|EG494640.1|EG494640
EST:     TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
genomic: TTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
EST: gi|125158332|gb|EL186977.1|EL186977
EST:     GGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAG                         CCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA
genomic: GGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaatt ... tcttatgcagCCATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT