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

gtattaatttgattctttgagaagtatgttttttcatttcttatattgatcttattgttccagcacaaattattcaaattgtagtactttagttttgatttggtaattgtttttcctattttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAGCCTGCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCG

Basic information

species Zea mays
transcript GRMZM2G118014_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g62640.4 (Oryza sativa), 3'ss of exon 5
gtattaatttgattctttgagaagtatgttttttcatttcttatattgatcttattgttccagcacaaattattcaaattgtagtactttagttttgatttggtaattgtttttcctattttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAGCCTGCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCG
|||||| |||||    ||||  | |||||  | ||  |||| |||    | |   | | ||||||||  | | |  ||| |||  | |  |||||| ||          |||||| |  |||| | |||||||||||  |||||||||| |||||||||||||||||||||||| |||||||| ||| | | |||||| ||||  |||  ||| |||| ||||| || |
gtattattttgaaagcttgaata-tatgtgctctcgattctcata---gtttgtgtataccagcacatgtaact--aatagta--aataaagttttaatcctactggcatttttctt-ctttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAGCCTACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTG
















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|71445995|gb|DR827045.1|DR827045
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|211063251|gb|FL401238.1|FL401238
EST:     GGCCCCAG-AAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTTACAAGGACAGAGCTTCATTAA
genomic: GGCCC-AGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAA
EST: gi|76284913|gb|DV024481.1|DV024481
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|211400936|gb|FL417155.1|FL417155
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|149079348|gb|EE168324.2|EE168324
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|211517989|gb|FL372294.1|FL372294
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|211387614|gb|FL172477.1|FL172477
EST:     AGCCCCAG-AAGTAGTGGAAGA-CTCAGAA-TAAAAGAGCTGATATGCAG                         GCTACCCNNTCT-GCT-GATGCTTTTAACA-GGACAGAGCTTCATTA-CTC
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCC--TCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTC
EST: gi|211311591|gb|FL416726.1|FL416726
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|211440987|gb|FL029795.1|FL029795
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAATGAGNTGATNTGCAG                         GCTACCCTNTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAC
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|76020071|gb|DT947241.1|DT947241
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
EST: gi|211019421|gb|FL374991.1|FL374991
EST:     AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG                         GCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG
genomic: AGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaattt ... tttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattgtagtactttagttttgatttggtaattgtttttcctattttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAGCCTGCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCG
                  ttttgat  putative branch site (score: 4)
                                ttgtttttcctatttt  putative PPT
             tttagttttgattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaatttgattctttgagaagtatgttttttcatttcttatattgatcttattgttccagcacaaattattcaaattgtagtactttagttttgatttggtaattgtttttcctattttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAGCCTGCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC