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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGACAAATGTTGTGATTTTCAGGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtctcattttcctgtgttaggcttgctgttgcacaaagtattgtctcactttgatttagctcactctttcctgactgactcacctgtgtcacag

Basic information

species Zea mays
transcript GRMZM2G009412_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009412_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 5'ss of exon 3
ATATGACAAATGTTGTGATTTTCAGGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtctcattttcctg--tgttaggcttgctgttg-cacaaagtattgtctcactttgatttagctcactctttcctgactgactcacctgtgtcacag
                         || || ||||||||||| |||||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||||    | | ||||| ||  |  |     |||     ||  ||  ||  ||| | |  ||  ||| |     |  ||  | ||  | | |   || ||      
-------------------------GCAAAAACCACCAAGAAGATCGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAGgtat--tatttcattgtcaagactccagagctgaaaattatcatgaatcattattttgctg-gatgtgttggatgctcacttgcataattgttctctgcag---

upper sequence: GRMZM2G009412_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g33921.1 (Oryza sativa), 5'ss of exon 3
ATATGACAAATGTTGTGATTTTCAGGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtctcattttcctgtgtt--aggcttgctgttg-cacaaagtattgtctcactttgatttagctcactctttcctgactgactcacctgtgtcacag
                         || || ||||||||||| |||||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||||    | | ||||| ||  |  |     |||     ||  ||  ||  ||| | |  ||  ||| |     |  ||  | ||  | | |   || || || ||
-------------------------GCAAAAACCACCAAGAAGATCGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAGgtat--tatttcattgtcaagactccagagctgaaaattatcatgaatcattattttgctg-gatgtgttggatgctcacttgcataattgttctctg-cagag

upper sequence: GRMZM2G009412_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 5'ss of exon 3
ATATGACAAATGTTGTGATTTTCAGGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtctcattttcctgtgttaggcttgctgttg-cacaaagtatt--gtctcactttgatttagctcactctttcctgactgactcacctgtgtcacag
                         || || ||||||||||| || ||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||||    | | ||||| ||  |  | | |||     ||| ||  ||  | |  || ||  |||   |  | |   |  |  || ||  | |    |   | ||||
-------------------------GCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAGgtat--tatttcattgtcaagactcaagctgaaaattgtcatgaatcaatcagtatctttttagatgtgttgggtgctatcttac--attattattctttacag

upper sequence: GRMZM2G009412_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 5'ss of exon 3
ATATGACAAATGTTGTGATTTTCAGGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtctcattttcctgtgttaggcttgctgttg-cacaaagtattgtctcactttgatttagctcactctttcctgactgactcacctgtgtcacag
                         || || ||||||||||| || ||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||||    | |  || | |   |  | | |||     ||  ||  ||  | | |||   || ||| |     |  ||  | |   | | |   |||||      
-------------------------GCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAGgtat--ttttgcaatgtgaagattcaagctgaaaattctcatgaatcagtatctt-tttagatgtgttggatgctcacttacataattattctgtgcag---

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|19436813|gb|BM953223.1|BM953223
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGATAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|14529377|gb|BI096510.1|BI096510
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGATAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|67022104|gb|CO450853.1|CO450853
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|33096235|gb|CF056229.1|CF056229
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACGTCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|32923496|gb|CF028308.1|CF028308
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|32944449|gb|CF049268.1|CF049268
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|166615670|gb|EG279121.1|EG279121
EST:     CTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGG
genomic: CTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGG
EST: gi|14208463|gb|BG842141.1|BG842141
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|19436812|gb|BM953222.1|BM953222
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGATAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|33094090|gb|CF054084.1|CF054084
EST:     GTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: GTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|19057470|gb|BM736122.1|BM736122
EST:     TGAAGCTGCAG-GCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGG-GCAAGCATTTTGAGATTGGTGGAGATAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|211127525|gb|FL066341.1|FL066341
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|4217819|gb|AI391815.1|AI391815
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|19057662|gb|BM736329.1|BM736329
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGATAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
EST: gi|32920410|gb|CF025222.1|CF025222
EST:     TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG                         AGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT
genomic: TGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtc ... tgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGACAAATGTTGTGATTTTCAGGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGgtgcagtgtctcattttcctgtgttaggcttgctgttgcacaaagtattgtctcactttgatttagctcactctttcctgactgactcacctgtgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC