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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatctatactgcattttcaacatgtatgtgtactgaaaacgatgttttgagatcaaagttgtaaaatgctctgaagatttataaaaggtgg...

Basic information

species Zea mays
transcript GRMZM2G178415_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g58040.1 (Oryza sativa), 5'ss of exon 5
ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatctatactgcattttcaacatgtatgtgtactgaaaacgatgttttgagatcaaagttgtaaaatgctctgaagatttataaaaggtgg-----------------------------------------------------------------------------------------
|||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| | | || | ||   | |||| | |||||   |||| ||| || |||||||  |    || |   ||         | |  || |||| |  |                                                                                           
ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatc-atgtctagcac-tttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataatgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaatacag

upper sequence: GRMZM2G178415_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 5'ss of exon 4
ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatctatactgcattttcaacatgtatgtgtac-tgaaaacga-tgttttgagatcaaagttgtaaaatgctctgaagatt-tataaaaggtgg
|||||||| ||||| ||||| ||||||||||| ||||||||  | || ||||||||||| || ||||| ||  | |||||  ||  |    |  ||  ||| |   ||  |  ||   ||    | | |  | | | |   ||   |        | ||| |||  | |     |  |
ACAATGGCTTGGATTCTTGATGAATACTCAAAATTCCATGGACATTCTCCTGCTGTTGTCACTGGAAAACCCATTgtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagcag

upper sequence: GRMZM2G178415_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 5'ss of exon 6
ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatc-----tatactgcattttcaa-catgtatgtgtactgaaaacgatgttttgagatcaaagttgtaaaatgctctgaagatttataaaaggtgg
|| |||||||||||||| || || ||||| || || ||||| |||||||||||||| ||||| ||||||||| | || || |  || |     |||  ||  ||   ||  |    | | |||   ||  |  | |||||  ||       |  ||   ||||  |||| |   |      
ACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATTgtgagtatatagcactcttatgatgggttgaaaagtacaggtttataccataattgtaggtttgatttcctgtagatgtaaatttctgctgattcaagta------

upper sequence: GRMZM2G178415_T02 (Zea mays), 5'ss of exon 5
lower sequence: EFJ06180 (Selaginella moellendorffii), 5'ss of exon 4
ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatctatactgcattttcaacatgtatgtgtactgaaaacgatgttttgagatcaaagttgtaaaatgctctgaagatttataaaaggtgg
|| ||||||||||| |||||||||||||| |||||||| || || || || ||  | || || ||||||||  | ||||||   | |||  |      | | |   |   |   |  |||  |     ||||    |     || | |                           
ACCATGGCATGGATTCTTGACGAATACTCTAAGTTCCACGGGTATTCGCCAGCAATAGTAACTGGAAAGCCACTTgtaagcttgtttcttgatgatgatgtgatttttccttgatgatgatgatataatttt----ttttgtttctcag--------------------------

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|148981458|gb|EE027657.2|EE027657
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|148934217|gb|EC878238.2|EC878238
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|60354014|gb|DN220987.1|DN220987
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTTGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|87152935|gb|DY397724.1|DY397724
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|22935999|gb|BU572274.1|BU572274
EST:     CTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAAGGGGAGTTCT
genomic: CTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAA-GCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAA-GGGGAGTTCT
EST: gi|19436213|gb|BM952623.1|BM952623
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAGGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGG
EST: gi|148940231|gb|EC885000.2|EC885000
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|20299950|gb|BQ162893.1|BQ162893
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|211300259|gb|FL012334.1|FL012334
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|78092010|gb|DV520384.1|DV520384
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|13125987|gb|BG316662.1|BG316662
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|78089717|gb|DV518091.1|DV518091
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|91867926|gb|EB399854.1|EB399854
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|149101283|gb|EE187396.2|EE187396
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|87156586|gb|DY401375.1|DY401375
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|149110227|gb|EE190296.2|EE190296
EST:     ACTCAAAATTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|19351039|gb|BM895571.1|BM895571
EST:     CTCAAAGTTCCATGGNTACTCACCNTGCTGT-GTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAG
genomic: CTCAAAGTTCCATGGTTACTCACC-TGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAG
EST: gi|19351121|gb|BM895653.1|BM895653
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|26559718|gb|CA831953.1|CA831953
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|60357158|gb|DN224131.1|DN224131
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatctatactgcattttcaacatgtatgtgtactgaaaacgatgttttgagatcaaagttgtaaaatgctctgaagatttataaaaggtgg

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT