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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctccagttggaatttaagtaggtgtactcagttttaagaaatatcgtatgatgctgacaagtttgcatcctgtgcag

Basic information

species Zea mays
transcript GRMZM2G466281_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g02750.2 (Oryza sativa), 5'ss of exon 4
ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctccagttggaatttaagtaggtgtactcagtttta--------agaaatatcgtat--gatgctgacaagtttgcatcctgtgcag
|||||||||||||||||||| ||||||||||| ||||||||||||||||||||| |||||||||| ||||||||||||| |||  | |   |||  || | |||| | | |||||||          || |   ||||  |||||||||| |  |  ||| ||  |||
ACTTTTGATGCTGTGGATGGTAAACAAGCAAGACGTACCAACTCATCAAGTCCTTTAGGCGAGCTATTTGACCACGgtagtctttactgaaaatacaacttggtgaattaagttttatccctttagaaagtcctgtatctgatgctgacatgactatatcttgaacag

upper sequence: GRMZM2G466281_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S269_30V6.1 (Physcomitrella patens), 5'ss of exon 6
ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatc--tccagttggaatt-taagtaggtgtactcagttttaagaaatatcgtatgat-gctgacaagtttgcatcctgtgcag----------------
|| ||||||||||| ||||| |||||||| ||||| || || || || |||||||| || || |||||||| |||||||| |      |||| | |  ||||  | ||     | || | ||  || | ||    | | | ||   |  |   | |  |||                 
ACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACGgtaaacagctttgttgaactcgtaagctgctg-gtggatttatcaggcatgttgtcccttagttcacttatcagtg-cgtaggcactcttacatatgtaaat

upper sequence: GRMZM2G466281_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S68_234V6.1 (Physcomitrella patens), 5'ss of exon 5
ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgta----atctccag----ttggaatttaa--gtaggtgtact-----cagttttaagaaatatcgtatgatgctgacaagtttgcatcctgtgcag---
|||||||||||||| ||||| || ||||| ||||| || ||||| || || ||||| || ||||||||||| |||||||    ||||   |    |   ||||| |  ||||   || |     ||    |    ||| ||||   ||  |    || ||   |  |||       
ACTTTTGATGCTGTTGATGGCAAGCAAGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatcttacggaactcacaatttgattgtagaaatattagagacatcactctacaatctcgttcaatattttttagattcgtttatgtatgtaaa

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|101388019|gb|EB816024.1|EB816024
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|76933447|gb|DV173462.1|DV173462
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|78108358|gb|DV526776.1|DV526776
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|76284393|gb|DV023961.1|DV023961
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|148930548|gb|EE285169.2|EE285169
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|84980730|gb|DW531079.1|DW531079
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|148948015|gb|EC893516.2|EC893516
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|149085392|gb|EE174899.2|EE174899
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|88756189|gb|DY540330.1|DY540330
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|24934262|gb|CA452480.1|CA452480
EST:     ACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: ACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|88756155|gb|DY540296.1|DY540296
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctccagttggaatttaagtaggtgtactcagttttaagaaatatcgtatgatgctgacaagtttgcatcctgtgcag

- - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT