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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctgtgcagtaatccgctctcgctcctctgatttcttatgttagtattttgctgttgctaggtagcagagatatgaaacggcattatgtcgtct...

Basic information

species Zea mays
transcript GRMZM5G850355_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G850355_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g42320.3 (Oryza sativa), 5'ss of exon 1
-----------------------CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctgtgcagtaatccgctctcgctcctctgatttcttatgttagtattttgctgttgctaggtagca-gagatatgaaacggcattatgtcgtct-
                       ||||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| |||||||||||| ||  | ||| || |||||  ||||  | ||   ||| | | | | || ||   |  |  |   ||  |   ||||| |     ||     | ||   | 
TTTTGTGGCGATTTCGTTTGCAGCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAGgtgcgtcccgtgaagcaatcccttctctatacttctattgcgt-tatgagaatcgagaaggggaggggaggtttgagattttggctggttcggt-tcacatg

upper sequence: GRMZM5G850355_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 2
CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctgtgcagtaatccgctctcgctcctctgatttcttatgttagtattttgctgttgctaggtagca-gagatatgaaacggcattatgtcgtct-
||||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| |||||||||||| ||  | ||| || |||||  ||||  | ||   ||| | | | | || ||   |  |  |   ||  |   ||||| |     ||     | ||   | 
CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAGgtgcgtcccgtgaagcaatcccttctctatacttctattgcgt-tatgagaatcgagaaggggaggggaggtttgagattttggctggttcggt-tcacatg
















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|15427202|gb|BI543024.1|BI543024
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32934694|gb|CF039506.1|CF039506
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211017640|gb|FL189740.1|FL189740
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|40337252|gb|CK371322.1|CK371322
EST:     GGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|22520740|gb|BU079551.1|BU079551
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|5566889|gb|AI881800.1|AI881800
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|14242859|gb|BG840665.2|BG840665
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211014870|gb|FL189739.1|FL189739
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAAGAAACTGCCTTCCTATTTT
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAA-GAAACTGCCTTC-TATTTT
EST: gi|211535545|gb|FL366410.1|FL366410
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32908069|gb|CF012882.1|CF012882
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|9254141|gb|BE344609.1|BE344609
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211408164|gb|FL390201.1|FL390201
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|87156656|gb|DY401445.1|DY401445
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|14203539|gb|BG837216.1|BG837216
EST:     CCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: CCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|9461620|gb|BE453822.1|BE453822
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211156517|gb|FL164231.1|FL164231
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|5456374|gb|AI834064.1|AI834064
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|31355634|gb|CD439991.1|CD439991
EST:     GGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAATGGTGTATTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|29167732|gb|CB410992.1|CB410992
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211017651|gb|FL189751.1|FL189751
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGT
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGT
EST: gi|8367928|gb|BE050873.1|BE050873
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAATGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|14204267|gb|BG837944.1|BG837944
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|12967998|gb|BG264945.1|BG264945
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211158124|gb|FL164253.1|FL164253
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211370171|gb|FL333604.1|FL333604
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32912475|gb|CF017287.1|CF017287
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211100498|gb|FL307608.1|FL307608
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|26559204|gb|CA831439.1|CA831439
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211352174|gb|FL343457.1|FL343457
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32906923|gb|CF011736.1|CF011736
EST:     GCACGCGCTCACTGTTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctgtgcagtaatccgctctcgctcctctgatttcttatgttagtattttgctgttgctaggtagcagagatatgaaacggcattatgtcgtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcgctcc