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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGTTGACCTTGGAACAGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccgcctccatatcacaagtcactttgatgctttgatcaaaacatggatatgaagagttgttttattgtgatttcag

Basic information

species Zea mays
transcript GRMZM2G050460_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050460_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 3
-------------------------------ACAATGTTGACCTTGGAACAGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccgcctccatatcacaagtcactttgatgctttgatcaaaacatggatatga-agagttgttttattgtgatttcag-------
                               | ||||| || || || ||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||   ||   | | | |  | |||   |   |     | | ||||||    || ||| ||   |  | ||   ||   |          
TGAAAAATAACAGCTATCTGTTTGTTTTCAGATAATGTCGATCTGGGGACAGCCTGTGGTAAATACTTCCGTGTTTGCTGCCTCAGCATTATTGATCCTGgtaacttcca--tacgtctacctagtatttgaaagaaactaaacaaaaccgttatttgatagtaatactgtacaatgcgcttgatttccag

upper sequence: GRMZM2G050460_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g16890.1 (Oryza sativa), 5'ss of exon 4
ACAATGTTGACCTTGGAACAGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccgcctccatatcacaagtcactttgatgctttgatcaaaacatggatatga-agagttgttttattgtgatttcag-------
| ||||| || || || ||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||   ||   | | | |  | |||   |   |     | | ||||||    || ||| ||   |  | ||   ||   |          
ATAATGTCGATCTGGGGACAGCCTGTGGTAAATACTTCCGTGTTTGCTGCCTCAGCATTATTGATCCTGgtaacttcca--tacgtctacctagtatttgaaagaaactaaacaaaaccgttatttgatagtaatactgtacaatgcgcttgatttccag
















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|211445721|gb|FL164466.1|FL164466
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCANGACTACACCGGGCGAGCAGTAAGGA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGA
EST: gi|15590487|gb|BI675103.1|BI675103
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|18164616|gb|BM334455.1|BM334455
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|211447832|gb|FL164470.1|FL164470
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|60354341|gb|DN221314.1|DN221314
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|44900176|gb|CK826721.1|CK826721
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|60358040|gb|DN225013.1|DN225013
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|116826202|gb|EC869965.1|EC869965
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTANCACCGGGCGAGCAGTAAGGATGGCAC
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTA-CACCGGGCGAGCAGTAAGGATGCCAC
EST: gi|18649989|gb|BM498808.1|BM498808
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|4887277|gb|AI677376.1|AI677376
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|15554273|gb|BI644271.1|BI644271
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|71772654|gb|DR970582.1|DR970582
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|12970901|gb|BG267215.1|BG267215
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|45567674|gb|CK985687.1|CK985687
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|4630652|gb|AI621526.1|AI621526
EST:     CTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: CTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|32912640|gb|CF017452.1|CF017452
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|45848107|gb|CN072050.1|CN072050
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|17921702|gb|BM259353.1|BM259353
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GNGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|9794654|gb|BE552962.1|BE552962
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|19822553|gb|BQ048577.1|BQ048577
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|71439472|gb|DR820522.1|DR820522
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|9824848|gb|BE575155.1|BE575155
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTAATGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCAC
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATT-CTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCAC
EST: gi|33101139|gb|CF061099.1|CF061099
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGACATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|78027496|gb|DV495883.1|DV495883
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|44681696|gb|CK786744.1|CK786744
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTGTCGATCCTG                         GTGATTCTGACATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|19057738|gb|BM736405.1|BM736405
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|7227589|gb|AW566230.1|AW566230
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|15590488|gb|BI675104.1|BI675104
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|37378408|gb|CF625893.1|CF625893
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA
EST: gi|211445722|gb|FL164467.1|FL164467
EST:     AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTG                         GTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGGCACA
genomic: AGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccg ... gtgatttcagGTGATTCTGATATCATCAAGACTACACCGGGCGAGCAGTAAGGATGCCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGTTGACCTTGGAACAGCCTGTGGAAAATACTTCCGTGTCTGCTGCCTCAGCATTATCGATCCTGgtaaaagccgcctccatatcacaagtcactttgatgctttgatcaaaacatggatatgaagagttgttttattgtgatttcag

- - - - - - - - - - - - - - - - - - - - - - TGCTGC