Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctggacaaagatcgcatatttagtcaattacgtctactcatcctttttcccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccag

Basic information

species Zea mays
transcript GRMZM2G018447_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018447_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 3
GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttt-tctggacaa-agatcgcatatttagtcaattacgtcta-ctcatcctt---tttcccttcat---ttcatttgattgaat---gatacataaccattcacgtcttttgcttccag
|||||| |||||||| |||||||||||||| || |||||||||||||| |||||| ||||||| |||||||||||||||||||| |||||||| ||||||||  | ||| | |  |||| ||||  | |  | |   |   || | ||  | ||||||   ||||   ||||   |||  |  |||  ||   | | || |   ||| |  |||||   ||||||
GGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCTCAGgtgagctttcttttcacaacagattactttctcatatagaaacctttaattaatcctttcgtttcttctcatctgttccctgcattcgatttggttgcaaactaatttaactctttca-ttccag

upper sequence: GRMZM2G018447_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G07810.1 (Glycine max), 5'ss of exon 3
GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctggacaaagat-cgcatatttagtcaattacgtctactcatcctttttcccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccag
|||  |||| |||||||||||  | || || ||||||||    |||||||||||| | |||||||| || |||||| |||| || |||||||| ||||||||     |||     |    || | || | |||  |  | |  | ||| |||  ||||    |||| |  || | || ||  | |  | |                        
GGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAATGAGACCTACCAGCTTCAGGTTGATTTTCCTGAGAATTACCCAATGGAGGCTCCTCAGgttcctcttttgtccctttcatacacaaaattaacctttgatttgtac-catg-ttttggttttcactg-atgttatcgacggttttacag-----------------------

upper sequence: GRMZM2G018447_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G36410.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctggacaaagatcgcatatttagtcaattacgtctactcatcctttttcccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccag
| | ||||| ||   |||||   | || || |||||||||   || || |||||  | || ||||| ||||||||||||||||||||||| || || |||||  | |  |||         |    |   || | ||  |    || |||||   |    ||      |   || ||  |  ||| | |||                      
GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcg-tcctctaact---ccttttgttaatacttaacgatacttaatcatcgcatcaatctcataacccgatggttccac-atataaaacag--------------------

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|211421813|gb|FL084940.1|FL084940
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424407|gb|FL084942.1|FL084942
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18163588|gb|BM333427.1|BM333427
EST:     AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18172273|gb|BM347661.1|BM347661
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|17929384|gb|BM266344.1|BM266344
EST:     ACCAGTTGCAGGTTGACTTCCNTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424413|gb|FL084948.1|FL084948
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCNATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|32869440|gb|CF009122.1|CF009122
EST:     ACCATTTTTTGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424415|gb|FL084950.1|FL084950
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421809|gb|FL084936.1|FL084936
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424416|gb|FL084951.1|FL084951
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76018971|gb|DT946141.1|DT946141
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|89756005|gb|DY686208.1|DY686208
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421806|gb|FL084933.1|FL084933
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424414|gb|FL084949.1|FL084949
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|29947193|gb|CB816528.1|CB816528
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76288121|gb|DV027689.1|DV027689
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|89246821|gb|DY618608.1|DY618608
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421814|gb|FL084941.1|FL084941
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|60352940|gb|DN219913.1|DN219913
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421802|gb|FL084929.1|FL084929
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18166490|gb|BM336329.1|BM336329
EST:     AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424417|gb|FL084952.1|FL084952
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76288120|gb|DV027688.1|DV027688
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421805|gb|FL084932.1|FL084932
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18169036|gb|BM338876.1|BM338876
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|116821688|gb|EC865015.1|EC865015
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCAACTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76018970|gb|DT946140.1|DT946140
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421808|gb|FL084935.1|FL084935
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctggacaaagatcgcatatttagtcaattacgtctactcatcctttttcccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG