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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag

Basic information

species Zea mays
transcript GRMZM2G027282_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgta---atttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag-----------------------------------------------------------------------
||| ||  | |||||||| ||||| |||||||||||||||||||| |||||||| || ||||| |||||||||||||||||||| || |||||||||||||||   |||| ||||  ||| ||   | | ||    |   | || |         |   | ||||    || ||| | |||||||  | || ||   |||  || |                                                                        
AGACACGCTACCTTCAGAATATGATTCACGGGTTAAGGCAATGGAGGTAGATGAAAAGCCTACAGAGGATTACAATGACATTGGTGGCCTTGAGAAACAGgtatttatttactttaaagatctaatgatgaaaacattagttaggatggtcaccat---tctgttgttatgtaagta-gcagtaacttcat-ttccatatctcataagtgttcatcagttgctgtttgttcattgttatctgctctcttatgttctacttttatattgtctaatgcag

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag
 |||||  ||||||| |||||||| ||  | |||||||| |||||||| ||||| || || || |||||||||||||||||||||||| | ||||| ||||| |   |||||   |  || |   | |  | ||  | ||    | || ||| || || | || ||||    |       | |   ||     |          
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtga---gcttt--ggttcttgccataatttattgaagcac--tttcttttgggggttaggta-attgatctctcaggtcatttcaatcaacag----------

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag-------------
 ||| |  ||||||| |||||||| ||||| |||||||| |||||||| ||||| || || || ||||| |||||||||||||| ||  | ||||| |||||    |    |     || |    || |  | |  |      ||  | || |  ||||   |  | |  | || |   |   |||||||     |||||   |             
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataatt----accgacaatttatcgatgcactctttctctttttctt-atttacaat-taggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcag--taatatgatg-tttggtataacacag---
 ||||| |||||||| |||||||| ||  | |||||||| |||||||| ||||| || || || ||||| |||||||||||||| ||| | ||||| ||||| |   |||||   |      |  |||| |    |||     |   |||| ||| || ||||   ||||| |   |||   | |   ||   ||||| |  | ||    
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtga---gcttt---ggttcttgccttaatt----tattgaagcccttgtt-tgggttagtta--atgcaatctctcaggtcatttcaataacttggtcttcctcaacag

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag
 ||||| ||||| || |||||||||||  ||||||| || ||||| || ||||| ||||| ||||| ||||||||||||||||| ||||| ||||| ||||||   || ||                 ||  || | | |   || ||||  ||  |||| | | | |  |  |   | | |  | || | ||| | |      
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgta---tgtttat---------------accattgtgttaat-ctgctgtattgactttgcttcgtagtgaa-actaattgagtttatttctggaacag-----

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 5'ss of exon 5
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggtta-actgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag
 || ||  | || || || ||||| || || || ||||| |||||||| ||||| || || ||||| ||||||||||||||||| || || ||||| ||||| | ||     |   |  |      || |  | |    |||   |  ||||        | | | | | |         |   || |       | |   ||||
GGACACTCTTCCGTCTGAATATGATTCTCGAGTAAAGGCTATGGAAGTCGATGAAAAGCCAACTGAAGATTACAATGACATTGGGGGTCTGGAGAAGCAGgtgaattttggactgaacatatttcatagagggattccccagggttcttgttacatgccagattcttcgtagttgtttcttttgataaatgcacttttgtaacag

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ15061 (Selaginella moellendorffii), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttat-atcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag
 |||||| | || || |||||||| || || || ||||| |||||||| ||||||||||| || ||||| |||| ||| ||||| || ||||| ||||| |||| | ||||        || |  ||   | || | ||||  |     ||  | |                                                 
GGATACACTTCCGTCCGAGTATGATTCTCGTGTCAAGGCTATGGAAGTCGATGAGAAACCCACAGAGGACTACAGTGATATTGGAGGGCTTGACAAACAAgtaact-gcttcatttctttgtgttttctttattctgatcaaaagcttggtgttag-------------------------------------------------

upper sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ37626 (Selaginella moellendorffii), 5'ss of exon 4
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttat-atcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag
 |||||| | || || |||||||| || || || ||||| |||||||| ||||||||||| || ||||| |||| ||| ||||| || ||||| ||||| |||| | ||||        || |  ||   | || | ||||  |     ||| | |                                                 
GGATACACTTCCGTCCGAGTATGATTCTCGTGTCAAGGCTATGGAAGTCGATGAGAAACCCACAGAGGACTACAGTGATATTGGAGGGCTTGACAAACAAgtaact-gcttcatttctttgtgttttctttattctgatcaaaagcttggttttag-------------------------------------------------

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|62550265|gb|DN830685.1|DN830685
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|148969904|gb|EE020805.2|EE020805
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|31355202|gb|CD439559.1|CD439559
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|60397914|gb|DN230730.1|DN230730
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|6527001|gb|AW216226.1|AW216226
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|61118361|gb|DN559322.1|DN559322
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|148967389|gb|EE018612.2|EE018612
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|60401214|gb|DN234021.1|DN234021
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|211379906|gb|FL296455.1|FL296455
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|149100602|gb|EE186689.2|EE186689
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|166596283|gb|EG233780.1|EG233780
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTAC
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTAC
EST: gi|20208194|gb|BQ134283.1|BQ134283
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCG
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCG
EST: gi|71448750|gb|DR829800.1|DR829800
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|74241540|gb|DT649454.1|DT649454
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|67041966|gb|CO468221.1|CO468221
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|26456217|gb|CA827800.1|CA827800
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCCAGAGCTTGTG
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTG
EST: gi|5268612|gb|AI770576.1|AI770576
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACNTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|6056527|gb|AW090917.1|AW090917
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|211086756|gb|FL006908.1|FL006908
EST:     TGAGAAACCTACTGAGGATTACAATGACATTAGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: TGAGAAACCTACTGAGGATTACAATGACATT-GGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|67017349|gb|CO446098.1|CO446098
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCATTAGTGTTACCAATGACACACCAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|148962495|gb|EE013359.2|EE013359
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTCACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|149089441|gb|EE178682.2|EE178682
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|31355810|gb|CD440167.1|CD440167
EST:     ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|6538999|gb|AW225138.1|AW225138
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
EST: gi|60352075|gb|DN219048.1|DN219048
EST:     ATGAGAAACCTACTGAGGATTACAATGACATCGGCGGACTTGAGAAACAG                         ATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA
genomic: ATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgct ... tataacacagATTCAAGAGCTTGTGGAAGCAATAGTGTTACCAATGACACACAAGGACCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT