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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatgtttaattttttccttctccatcaatctatccctatatcactttgactgcggaaaatcatgggcatgtgcatcttggcattgatgaagtgt...

Basic information

species Zea mays
transcript GRMZM2G174286_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 6
ATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgt--aatccatgtttaattttttccttctccatcaatctatccctatatcactttgactgcggaaaatcatgggcatgtgcatcttggcattgatgaagtgt-----
|||||  ||||| ||||| | |||||||||||||||||| ||||| |||||||||| ||||||||||||||||||  |||  ||||||  ||||   | |||||| ||||  ||   | | | |  |  ||   ||||| | | |||||| ||||||    ||||  |    ||      
ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgtttgctttt---cctctccagcaattcata--tgttttaagtgaacataggaaattta-gggcatatgcatcc-atcatttctactatgctgttt

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

upper sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 7
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 5'ss of exon 6
ATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaa---tccatgtttaattttttccttctccatcaatctatccctatatcactttgactgcggaaaatcatgggcatgtgcatcttggcattgatgaagtgt
||    || |||||||||||||||||||| || ||||   ||||||| ||| | || |||||||||||||||||||    |  | || ||  |  ||  ||   ||   ||  ||   | ||   |  |   ||    |  || || | ||||  ||    |              
ATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATCATTTCTAAGATGTTCTTTGCAGgtatagtttgaagtatagatcatt--ttacacagagattgatttttttaatgcactctatgtctcatctcttgtgaatgtatattgcag--------------

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|93284395|gb|EB676659.1|EB676659
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|149112907|gb|EE295706.2|EE295706
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|88754539|gb|DY538680.1|DY538680
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|24765679|gb|CA400838.1|CA400838
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|71300276|gb|DR786208.1|DR786208
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|28985354|gb|CB350599.1|CB350599
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|78106688|gb|DV525106.1|DV525106
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|45846980|gb|CN070923.1|CN070923
EST:     TCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCCCTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: TCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|18174253|gb|BM349641.1|BM349641
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|67017793|gb|CO446542.1|CO446542
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|67020535|gb|CO449284.1|CO449284
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
EST: gi|37383767|gb|CF628916.1|CF628916
EST:     GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG                         GTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG
genomic: GTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatg ... tgtttttcagGTGTATCACTATTTGCAGCCCTCGGGTTTGTTCTCTATGGAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgtaatccatgtttaattttttccttctccatcaatctatccctatatcactttgactgcggaaaatcatgggcatgtgcatcttggcattgatgaagtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG