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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatttcattgtgatagaaatttacacactctgtactcttctggtactctttgaatgattgactctatagagtctagaaaataaatattagtctttattcag

Basic information

species Zea mays
transcript GRMZM2G124502_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124502_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g56980.1 (Oryza sativa), 5'ss of exon 2
TAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtact---aaatttc----attgtgatag--aaatttacacactctgtactcttctggtactctttgaatgattgactctatagagtctagaaaataaatattagtctttattcag
 ||||| ||| ||||||| ||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||||| ||||||||||||||||||| |   |  ||||    |||||  |||  ||| |  ||  |  | || || | || ||  || |   | | ||| || |  ||| |   ||| ||| |      ||  ||||||
AAAGCGGAAACGAGGTGGGCCTGGTGGTTTAAATAAAGTTTGTGCAATCTCACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGAACTCAGgtaatctcagctttccccaattgtattagagaaaatggcatccaatttaatcctgtgataaactct---ttaatgaatcaaccgagac---aaagtaacttgcttcctccattcag

upper sequence: GRMZM2G124502_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G39530.1 (Glycine max), 5'ss of exon 2
TAAGCGAAA-AAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatttcattgtgatagaaatttacacactctgtactcttctggtactctttgaatgattgactctatagagt---ctagaaaataaatattagtctttattcag-----------------------
 |  | ||| |||||||||  |||||||| |||| |||||||| |   |||| |||||||||||| |  ||||||||||| | || ||| |||||||| ||||| |    ||     | |   |  |  |  | ||||  | |    ||  |     |||||  |    | | |  | |   | |   | |||  |  |   | | ||                          
-AGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaaccactgattaagaaacaaattcttttggaacacttttatatgctcaattcag

upper sequence: GRMZM2G124502_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv19s0090g01460.t01 (Vitis vinifera), 5'ss of exon 2
TAAGCGAAA-AAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatttcattgtgatagaaatttacacactctgtactcttctggtactctttgaatgattgactctatagagtctagaaaataaatattagtctttattcag
 ||   ||| ||||||||| || || ||| |||| ||||||||||   ||||||||||||||||||||||||||||  || | ||  || |||| ||  ||||   | |||     || | ||| || | |  |  |  |  | | |  ||  | | | | |   | |   ||| |     |   |||    | ||   ||  |||||
-AACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTGCCAAGGACCGAGgt-tcagattc----gtaaaagatatatccttaa-cgattgtttgccagttttatatcatttcctaatattattgg---catctaatttccaatatgtttggttcag

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|74239586|gb|DT647500.1|DT647500
EST:     CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAG                         ATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatt ... ctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
EST: gi|78111193|gb|DV529590.1|DV529590
EST:     CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAG                         ATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatt ... ctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
EST: gi|71422220|gb|DR805652.1|DR805652
EST:     CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAG                         ATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatt ... ctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
EST: gi|71440370|gb|DR821420.1|DR821420
EST:     CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAG                         ATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT
genomic: CACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatt ... ctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGAACTCAGgtactaaatttcattgtgatagaaatttacacactctgtactcttctggtactctttgaatgattgactctatagagtctagaaaataaatattagtctttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC