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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtattgtccaacatattgtcaagcatcctttgttgcttcttgagagctgaactctttcttcctctattttcttacag

Basic information

species Zea mays
transcript GRMZM2G146697_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146697_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g68750.1 (Oryza sativa), 5'ss of exon 5
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtattgtccaacatattgtcaagcatcc------tttgttgct-----tcttgagagctgaactctttcttcctctattttcttacag-
 ||||| ||||| |||||||| ||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||||||||||||||| |   ||| ||| |   |     | ||||  ||||         |||  | ||     | || | ||  || |  ||  |||  ||| ||  ||||   
TATGATTAACATCACTGATCACCATTACAAGACAGAAATTGCATCTCGTTGTGTTGAGCTAGCAGAACAATTTGCACCTAGCAATCAGTGGTTCATCCAGgtgacagcatcagtctatgcatgtttgttgttgagcacttaatgtattttctactaatatttttaacagaagatcctttggttctactaattatttaccag

upper sequence: GRMZM2G146697_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G35650.1 (Glycine max), 5'ss of exon 4
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtattgtccaacatattg--tcaagcatcctttgttgc------ttcttgagagctgaactctttcttcctctattttcttacag
|||||| | ||||| |||| | |||||||| ||  | || ||||| || ||||| |||||||| ||||||||||| || || ||||| ||||| || ||||||||   |  |||    || |   |||||  |  |   |  |||| |||      |  |||| | || ||   | |||     |||  |  | |||
CATGATTAGCATAAGTGATGACCATTATAAAACTTATATAGCATCTCGATGTGTGGAACTTGCTGAGCAATTTGCACCAAGTAATCATTGGTTTATACAGgtaattgaaatagttgcctcaatattattgattttacatttttttgatgcatacattcattgataact-aataatatctggtattatggttatgcag

upper sequence: GRMZM2G146697_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G20260.1 (Glycine max), 5'ss of exon 4
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtat-----tgtccaacatattg--tcaagcatcctttgt---tgcttcttgagagctgaactctttcttcctctattttcttacag
|||||| | ||||| |||| |||||||||| ||| | || ||||| || ||||| |||||||||||||||||||| ||||| ||||| ||||| || ||||||||    |   |       ||| |   || |||  | |   ||  ||||       |  |||| | |  ||   |  |||  ||| |  | || |||
CATGATTAGCATAAGTGATGATCATTATAAAACATATATAGCATCTCGATGTGTCGAACTTGCAGAGCAATTTGCTCCTAGTAATCATTGGTTTATACAGgtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataacc-aataataccttgttctttgattttgcag

upper sequence: GRMZM2G146697_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G08320.1 (Glycine max), 5'ss of exon 4
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtatt-----gtccaacatattg--tcaagcatcctttgt---tgcttcttgagagctgaactctttcttcctctattttcttacag
|||||| | ||||| |||| |||||||||| ||  | || ||||| || ||||| |||||||||||||||||||| ||||| ||| | ||||| || ||||||||    |   |  |     || |   || |||  | |   ||  ||||       |  |||| | |  ||   |  |||  ||| |  | || |||
CATGATTAGCATAAGTGATGATCATTATAAAACCTATATAGCATCTCGATGTGTCGAACTTGCAGAGCAATTTGCTCCTAGTAATTATTGGTTTATACAGgtaatggtgttgttgcttttatgttcttgattttgaattagttattttttgcaaacattcattgataacc-aataataccttgttctttgattttgcag

upper sequence: GRMZM2G146697_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT1G31730.1 (Arabidopsis thaliana), 5'ss of exon 4
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtattgtccaacatattgtcaagcatcc------tttgttgcttcttgagagctgaactctttcttcctctattttcttacag
|||||| |  || |  ||  ||||||| || || || || ||||| |||||||||||  | || || |||||||| || |||||||| |||||||||||||||   |    |      |   |  | | | |   ||         | |  |  || ||     | ||| | |  ||   ||| |  |       
CATGATTAGTATCAACGACAATCATTACAAAACTGAGATAGCATCTCGTTGTGTTGAGTTGGCCGAACAATTTGCTCCAAGCAATCAATGGTTCATCCAGgtagcaagccaacctccattgtaactgtggcctgacaataaacatatatactctttgtttctgacagaagtttaactgtttctgtactgcag---

upper sequence: GRMZM2G146697_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 5'ss of exon 5
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagta--ttgtccaa--catattgt-caagcatcctttgtt---gcttcttgagagctgaactctt----tcttcctctattttcttacag
|||||| | ||| | |||| ||||||| || || ||||| ||||| || ||||||||||| |||||||||||||| || ||||| || ||||| ||||||||||| | ||   |   || ||||   || |||||  | | |    ||| |   | || || |    | ||  |||    | |  |  ||| |  ||||||
CATGATAAGCATTAATGATAATCATTACAAAACTGAAATAGCATCTCGATGTGTTGAACTGGCAGAGCAATTTGCACCAAGCAACCATTGGTTTATCCAGgtaattatattgttgccttttccattccagattgtatatgaacgggttgcttgtgtttttttaccttttaatgcttagattttctccttatgtgtttacag

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|211306615|gb|FL245975.1|FL245975
EST:     GTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAG                         ACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTG
genomic: GTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacat ... tttcttacagACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTG
EST: gi|89762346|gb|DY689972.1|DY689972
EST:     GTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAG                         ACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTG
genomic: GTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacat ... tttcttacagACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTG
EST: gi|9952284|gb|BE638867.1|BE638867
EST:     GTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAT                         ACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTG
genomic: GTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacat ... tttcttacagACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGATCAACATAACTGATCATCATTATAAGACAGAAATTGCATCACGTTGTGTTGAACTTGCAGAGCAATTTGCGCCTAGCAATCAGTGGTTCATCCAGgtaatcacatgagtattgtccaacatattgtcaagcatcctttgttgcttcttgagagctgaactctttcttcctctattttcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA