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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTGCTGAACACGGAGCAGCCCATCGCGGAGCGCTTCCGGGCGCTCTTCTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctcgcttcactgaatcggctttgctactcttcaaagcttggtcgaaggctttagcagcttgtggatttagcaacagatttctggtccctgctg...

Basic information

species Zea mays
transcript GRMZM2G101502_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101502_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g43100.1 (Oryza sativa), 5'ss of exon 1
CGGCTGCTGAACACGGAGCAGCCCATCGCGGAGCGCTTCCGGGCGCTCTTCTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctcgcttcactgaatcggctttgctactcttcaaagcttggtcgaaggctttagcagcttgtg-gatttagcaacagatttctggtccctgctg------
|| |||||  || ||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||| || || || ||||||||||||||||||||||||  |    |   || |  ||   || ||  ||| |     ||   |    ||||| |   |    | ||| |      || | || |   | ||| |      
CGCCTGCTCGACGCGGCGCAGCCCATCGCCGAGCGCTTCCGGGCGCTCTTCTCCCTCCGCAACCTCCGCGGCGACGCCCCTCGCCGCGCCCTCCTCCAAGgtctccccctcgtcggctcacccg--cttacttgtctcc-----ttatgcagcagctttggtttccaccgtgatatgattcaaggtctcagtagcttgccgacttgg

upper sequence: GRMZM2G101502_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g06620.1 (Oryza sativa), 5'ss of exon 2
CGGCTGCTGAACACGGAGCAGCCCATCGCGGAGCGCTTCCGGGCGCTCTTCTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctcgcttcactgaatcggctttgctactcttcaaagcttggtcgaaggctttagcagcttgtggatttag--caacagatttctggtccctgctg------------------------------------
| ||||||  ||||||  ||||||||||| || |||||||| |||||||||||||||||||||||||  || ||||  || ||| |||||||||||||||||||   ||| ||  ||| |  |     |   | |  | |||||||| |     |    |     |  | |||  ||   |  ||| |   ||  | |                                        
CTGCTGCTTGACACGGCACAGCCCATCGCTGAACGCTTCCGTGCGCTCTTCTCCCTCCGCAACCTCCATGGTGATGGCCCCCGCTGCGCCCTCCTCCAAGgtcttacctcacta-actcacccactcatatcaatgat-aaagcttgttgtttagtgacaattattcattgatgaagactactagaataaaggagctttagaaagctaatatatttgactgtttgatgcattgctcag
















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|76914577|gb|DV165582.1|DV165582
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|78106816|gb|DV525234.1|DV525234
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|38687697|gb|CK144728.1|CK144728
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|211413922|gb|FL311395.1|FL311395
EST:     CTCCCTCCGCAACCTCAGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|78092612|gb|DV520986.1|DV520986
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|76909001|gb|DV163174.1|DV163174
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|78078333|gb|DV506748.1|DV506748
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|78115922|gb|DV534310.1|DV534310
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|93016960|gb|EB642480.1|EB642480
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|89757602|gb|DY687134.1|DY687134
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|38687442|gb|CK144473.1|CK144473
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAATGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|211420491|gb|FL364948.1|FL364948
EST:     CTCCCTCCGCAACCTCAGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCSRAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTT
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGC-AAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTT
EST: gi|76293315|gb|DV032883.1|DV032883
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|211080959|gb|FL340060.1|FL340060
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|74236078|gb|DT643992.1|DT643992
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|149014196|gb|EE043749.2|EE043749
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|67019156|gb|CO447905.1|CO447905
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|211327094|gb|FL352861.1|FL352861
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|211270705|gb|FL364933.1|FL364933
EST:     CTCCCTCCGCAACCTCAGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
EST: gi|76929289|gb|DV171943.1|DV171943
EST:     CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAG                         CTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG
genomic: CTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctc ... aattgttcagCTGCAAGGGATCCTTCTAACTTGCTTGCCCATGAGGCTGCATTTGCACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTGCTGAACACGGAGCAGCCCATCGCGGAGCGCTTCCGGGCGCTCTTCTCCCTCCGCAACCTCCGCGGGGATGCGCCGCGCCGCGCCCTCCTCCAAGgtctcgtctcgcttcactgaatcggctttgctactcttcaaagcttggtcgaaggctttagcagcttgtggatttagcaacagatttctggtccctgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC