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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgcaagttacttctagaagtgctttccaattttctaacagcgtcaatttttaatcctaatctcgtacttaaatctttagtgtaaatctagccc...

Basic information

species Zea mays
transcript GRMZM2G165418_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 4
GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgcaagttactt-----ctagaagtgctttccaa--ttttctaacagcgtcaatttttaatcctaatctcgtacttaaatctttagtgtaaatctagccc
|||||||||||| |||||||||| ||||| |||||||||||||||||| ||| | ||||||||| ||||||||||||||||||||||||||||||||||||||||||   || |   ||     | || | || ||| |||  |||    |   |   |  |||  |  ||||| |   | ||||  ||   || |  | | |    
GGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggagaaaaatatgttaggacccaggaatggttttcaagatttctgcatgccaatatctttctaatctaatgtaacatttaagcct---gtcttgaccaa----

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 4
GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgcaa--gttacttctagaagtgctttccaattttctaacagcgtcaattt-ttaatcctaatctcgtacttaaat-ctttagtgtaaatctagccc-
|||||| || || || |||||||  ||||  |||||||| | ||| ||   ||| |||| |||| | |||||||||||||||||||| ||||  ||||||||||| |   ||   | || | ||| | ||||||  | |  | | |     ||||||  || ||   |||   | ||     | |  |  ||   | |||     
GGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATAAAACAATCAAATTTTGGAAGgtatgaaatgaatgatcacctttagca-tgctttt-agtgctgtcatt-tatcaattcattgata--aattgtgcacaaggttgcacttctgaggaactaagttt
















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|31352864|gb|CD437221.1|CD437221
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211384019|gb|FL015614.1|FL015614
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|78112474|gb|DV530868.1|DV530868
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|50332602|gb|CO527728.1|CO527728
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|148945029|gb|EC890213.2|EC890213
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|9732635|gb|BE511387.1|BE511387
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211384022|gb|FL015617.1|FL015617
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAAATTTGGACAGNTC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA-TTTGGACAGTTC
EST: gi|71419454|gb|DR804774.1|DR804774
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|19822590|gb|BQ048614.1|BQ048614
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|149084056|gb|EE173454.2|EE173454
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGAAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA
EST: gi|19822589|gb|BQ048613.1|BQ048613
EST:     ATGCTCTCTCCCTTTTGNCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211386656|gb|FL015629.1|FL015629
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211384020|gb|FL015615.1|FL015615
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAAATTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgcaagttacttctagaagtgctttccaattttctaacagcgtcaatttttaatcctaatctcgtacttaaatctttagtgtaaatctagccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG