Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgatttactattctggtgcccaagtaattgacttatagttcacaattgcattgagtaatcaaacttgatgtgaatgccgatccatgcttgcagc...

Basic information

species Zea mays
transcript GRMZM2G016184_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016184_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 5'ss of exon 2
TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgatttactattctggtgcccaagtaattgacttatagttcacaatt-gcattgagtaatcaaacttgatg-tgaatgccgatc-catgcttgcagc------
 |||||||| ||||||||||  |||||||| |||||  |||| ||||||||||| |||||||||||||| |||||| | ||||||| ||| ||||||||||||  ||    |  | || | ||  | |         ||| |  || |  ||| |||||| | |||||  |   ||| |     |||||  |||| |||          
GTACAAGTACCAAGCTCAGGAGTTGATGAGAGACTACTTGCTGGCTGATCCACTGGTTCCGTACACCTCGGTGCTCGTAGGCATTGCCCTGTGCAAGATGgtaatttcgcctgttcttgtagtttctac--------cttgtgcttgatgatttgcattgcggaatcag-cgcaatgcttgtcaccgattgcatgtttgtgctgtgttg
















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|32832303|gb|CD971981.1|CD971981
EST:     ACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCGCTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: ACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211446537|gb|FL323006.1|FL323006
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATT
EST: gi|211179443|gb|FL364371.1|FL364371
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211370346|gb|FL342982.1|FL342982
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211367569|gb|FL335348.1|FL335348
EST:     CACTAGTTCCGTWCACCTCTGTGCTCATTGGCATTGTCCTYTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCC
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCC
EST: gi|211430478|gb|FL350076.1|FL350076
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|44681921|gb|CK786969.1|CK786969
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|76293603|gb|DV033171.1|DV033171
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211134109|gb|FL315814.1|FL315814
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTCAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|148947020|gb|EC892317.2|EC892317
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|76286797|gb|DV026365.1|DV026365
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211200884|gb|FL351309.1|FL351309
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|50322746|gb|CO517872.1|CO517872
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|50338098|gb|CO533224.1|CO533224
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211235414|gb|FL352706.1|FL352706
EST:     ACTAGTTCCGTACACCTCTGTGCTCATTTGGCATTGTCCTCTGCAAGATG                         GCTTTACGATTTCACTCG
genomic: ACTAGTTCCGTACACCTCTGTGCTCATT-GGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTT-ACGATTTCACTCG
EST: gi|148953653|gb|EC899012.2|EC899012
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211176856|gb|FL323774.1|FL323774
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTCAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|76280960|gb|DV020528.1|DV020528
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgatttactattctggtgcccaagtaattgacttatagttcacaattgcattgagtaatcaaacttgatgtgaatgccgatccatgcttgcagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG