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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactctgtatgtccacattctaaagggcttggtcattgcgatgccaaatacttatattttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacag

Basic information

species Zea mays
transcript GRMZM2G435373_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 9
TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactctgta-tgtccacattctaaagggcttggtcattgcgatgccaaatacttatat---tttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacag
|||||| |||||||| |||||||| ||||| || || || ||||||||||||||||| |||||||| || || ||||||||||| || ||||| |||||||| |||  ||| |  |||   || | ||     |      |||    | |   ||  | || |    || |||||||     ||    | || |||   ||     |  || |        |  ||||     |       |   |   ||||  ||| |     | |||||  ||   |       ||| | |||||
TGAATTTGATATGGAAGGGAAAGTCTGTGGCGTTACTTCAGAAGGTGAAACTGCAAAATGCAAGAAAGTTGTTTGTGATCCTTCATACTTACCTAACAAGgttaattttctttcctgtattcaatttatttaccacatgaattttctttcagtatgttcatttaggattcctagatgatgtacttccat-cttaacacattcacagcaaatttactattttttcttcttcccttccatttgttgagaagttttattaactacaaccacatttgatgttctgtatacatttattaacag

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 9
TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactctgtatgtccacattctaaagggcttggtcattgcgatgccaaatacttatattttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacag
|||||| |||||||| |||||||| || || || ||||| ||||| ||||||||||| |||||||| || || ||||| ||||| || ||||| |||||||| |||  ||| |    |   ||||   |  |  | ||  ||   ||      | ||   || ||  || ||| ||   |   |  |   |  ||     ||    |          |  ||||     |       |       ||||  ||| |     |||||||  ||   | ||   |||| | |||||
TGAATTTGATATGGAAGGGAAAGTCTGCGGCGTTACATCAGAAGGAGAAACTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttcttt---cctgtattcagcacaggattgttcttttaatatgttcttctgggatatt--taaatgtcatattccatctcaagatattcacaattgaacttactgtgtttttcttctgcccttccatttgttgataagttttattaactgcaacctcatttgatgttctgcttacgtttattaacag
















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|6031345|gb|AW076202.1|AW076202
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAAT
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAAT
EST: gi|24934285|gb|CA452503.1|CA452503
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|67031426|gb|CO460175.1|CO460175
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|33095264|gb|CF055258.1|CF055258
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|32856054|gb|CD995735.1|CD995735
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|47962286|gb|CN844995.1|CN844995
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|33102234|gb|CF062194.1|CF062194
EST:     AAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: AAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211034436|gb|FL381555.1|FL381555
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211445979|gb|FL406296.1|FL406296
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211259815|gb|FL426651.1|FL426651
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|32919393|gb|CF024205.1|CF024205
EST:     GCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: GCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211346475|gb|FL413228.1|FL413228
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactctgtatgtccacattctaaagggcttggtcattgcgatgccaaatacttatattttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG