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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagcttcgatcctatcgatacactctttctatataatccatagtgcctgtctcacctctcttgcgaattttatatttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G02180.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g02850.1 (Oryza sativa), 5'ss of exon 6
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagcttcgatcctatcgatacactctttctatataatccatagtgcctgtctcacctc---tcttgcgaattttatatttgcag----------------
||    || ||| |||  ||||||||||| || |||||||  ||||| ||| | ||||||||||||||||||||||| |  |||   |   ||        |||| |  | || |    | |   | | |    |     |||| | |  | |||  || ||                
ATAATACTTTGGATGGCGTTGTGGTGGAAACCAGTTCGAGCAATGGTCATCTTGTCTAAGATGTTCTTTGCAGgtaaat--ctt--gtgtaatttgccttgtcttgcagt-tagtatggattttttattttgaatgagagcttgtggaaatcatagctggagatagatgggaaaacta

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 6
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaa---ttagcttcgat---cctatcgatacactctttctatataatccatagtgcctgtctcacctctcttgcgaattttatatttgcag--------
||     ||||| ||||| | |||||||| || |||||||||||| | ||| | || |||||||||||||||||||    |||  || | |   ||| || |   | || |    | |||   |   |       | |   |   |||     | || | | |          
ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgtttgcttttcctctccagcaattcatatgttttaagtgaacataggaaatttagggcatatgcatccatcatttctactatgctgttt

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 7
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaat-------tagcttcgatcctatcgataca-ctctttctatataatccatagtgcctgtctcacctctcttgcgaattttatatttgcag------
||    ||||||||||||||||||||||| || |||||| ||||||| ||| | || |||||||||||||||||||||       ||  ||    | | || ||  | || |  |||||| |     | |||             | || | || ||    |||  |      
ATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatgtttaattttttccttctccatcaatctatccctatatcactttgactgcggaaaatcatgggcatgtgcatcttggcattgatgaagtgt

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G003076_T03 (Zea mays), 5'ss of exon 6
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagcttcgatcctatcgatacactctttctatataatccatagtgcctgtctcacctc----tcttgcgaattttat-atttgcag----------
||   ||||||||||||||| |||||||| || |||||||||||||| ||  |  | ||||||||||||||||||| |     |       ||  ||   |||  || || |  |     || ||| |  || |      || || | || ||   ||||  |           
ATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAGgtattccatgtttcattaattcattt-ctccatcaatctctttttatgtccctatgacagcatgagatcatgggcatcttgccatttataaagtgcgatta

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G003076_T02 (Zea mays), 5'ss of exon 6
--------------------ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagcttcgatcctatcgatacactctttctatataatccatagtgcctgtctcacctc----tcttgcgaattttat-atttgcag----------
                    ||   ||||||||||||||| |||||||| || |||||||||||||| ||  |  | ||||||||||||||||||| |     |       ||  ||   |||  || || |  |     || ||| |  || |      || || | || ||   ||||  |           
TTGACATCAATGTATTTCAGATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAGgtattccatgtttcattaattcattt-ctccatcaatctctttttatgtccctatgacagcatgagatcatgggcatcttgccatttataaagtgcgatta

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 6
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagcttcgatcctatcgatacactctttctat-----ataatcc------atagtgcctgtctcacctctcttgcgaattttatatttgcag
|||||| | ||||| ||||| |||||||| ||| | | | |  || | |||||||||||||||||||||||||||  |      | |  | || |||    | || | ||      || | |      ||  |  |||   || || ||||   ||    |||| |||||
ATTGCTATGTGGTTTGTTTTATGGTGGAAACCTATCCCAATCGTGTTCATCCTATCTAAGATGTTCTTTGCAGgttttgcttcactacacaatagatgatttgttgcaattctcagtagttcctcttgatgattactgatacaactttcttttaaacaa-atatctgcag

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|19877197|gb|AU238028.1|AU238028
EST:     GTGGAAGCCNGTTCGAGTTATGGNAATCCTATCTAAGATGTTCTTTGCAG                         GTGTTTCATTG
genomic: GTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagct ... atatttgcagGTGTTTCATTG
EST: gi|124891743|gb|EH970645.1|EH970645
EST:     TAATCCTATCTAAGATGTTCTTTGCAG                         GTGTTTCATTGTTCGCTGCCCTTGGATTTTTACTTTATGGTGGAAG
genomic: TAATCCTATCTAAGATGTTCTTTGCAGgtaattagct ... atatttgcagGTGTTTCATTGTTCGCTGCCCTTGGATTTTTACTTTATGGTGGAAG
EST: gi|124704210|gb|EH795612.1|EH795612
EST:     GGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATAGTTACTTTGCAG                         GTGTTTCATTGTTCGCTGCC
genomic: GGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGAT-GTT-CTTTGCAGgtaattagct ... atatttgcagGTGTTTCATTGTTCGCTGCC
EST: gi|125239537|gb|EL253622.1|EL253622
EST:     TAATCCTATCTAAGATGTTCTTTGCAG                         GTGTTTCATTGTTCGCTGCCCTTGGATTTTTACTTTATGGTGGAAG
genomic: TAATCCTATCTAAGATGTTCTTTGCAGgtaattagct ... atatttgcagGTGTTTCATTGTTCGCTGCCCTTGGATTTTTACTTTATGGTGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaattagcttcgatcctatcgatacactctttctatataatccatagtgcctgtctcacctctcttgcgaattttatatttgcag

- - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG