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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataaaattcttctctgcttctatttattctcttcaacatgtgctactcctattaatttctctttcccttttatatttgcag

Basic information

species Zea mays
transcript GRMZM2G055020_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 5'ss of exon 4
GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataaaattcttctctgcttctatttattctcttcaacatgtgctactcctattaatttc-tctttcccttttatatttgcag
|| ||||||||||||||||||||||| ||||||||| |||| || |||||||||||||||  ||||||||||||||| || |||||||||||||||||||  |||  |   | |   | |  | | ||  ||  ||| ||||||  |  | | |||||||||  ||||||   || || |||  ||
GCCCAGCTTGAGAAGATTGCTCCAACTTGGATGAATATTTCGTTGAAAATGAAAGAGGATGTGGAGACAGACAAAGCTTTTGGATGGGTCTTGGAAATgtcggtactattatgtgtacagtatttcttc-ttgacttaaacatgcacaccccttattaatttgatctttcatattcatgtttatag

upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G26610.1 (Glycine max), 5'ss of exon 5
GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataaaattcttctctgcttc-tatttattctcttcaacatgtgctactcctattaattt-ctctttcccttttatatttgcag----------------
| |  | |||  |||||||| || || ||||||||| |||| || || |||||||||||||  ||||| || ||||| || ||||||||  | |||||||  || | |        |||| |   ||||| |  | |  || | ||  |    ||  || ||| ||  ||    || ||  ||                    
GATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAATgtatgtcttaccaaaaaatctgatagatatttttgttttagaagaggtattggaactgatagttttctgctttatgttaatgattttttttcttgtggagccaag

upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G44810.1 (Glycine max), 5'ss of exon 6
GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtat------aaaattcttctctgcttctatttattctcttcaacatgtgctactcct-attaattt---ctctttcccttttatatttgcag---------------------------------------------------------------
 ||  | | ||| | || ||| | || ||| | ||||||||||| | ||||||||| ||||| ||||| || ||||| || ||||||||  | ||||||| |||||      | || |   |       | |||      |||||   | |  || |  | ||| | |     ||||| | ||||||| ||                                                                   
TCTTTGATGGAGGAAATAGCTTCCACATGGGTAAATGTTTCATTGAGAATGAAAGATGATCAAGAGACTGATAAAGCTTTTGGATGGGTGCTTGAAATgtgagtattaccatagaaattcacgaattcacgattcggaggcttcattttttattatttatcatttactgatgttcttttcattttataatttttcctggaccgtggtctgtattaataggtctaaccttctgctgctttgattctctgttgagtaaag

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|5468725|gb|AI834516.1|AI834516
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|71761576|gb|DR959513.1|DR959513
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|5895926|gb|AW037172.1|AW037172
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|74237664|gb|DT645578.1|DT645578
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|78082143|gb|DV510555.1|DV510555
EST:     ATGAAAGAGGATCGGGAGACAGACAAAGCATTCGGATGGGTTTTGGAAAT                         GTACGCATACGCTGTTGTTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|76015780|gb|DT942950.1|DT942950
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|5686756|gb|AI939849.1|AI939849
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|211541009|gb|FL454732.1|FL454732
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|76917228|gb|DV166719.1|DV166719
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|71763634|gb|DR961571.1|DR961571
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|60347170|gb|DN214143.1|DN214143
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|78023550|gb|DV491937.1|DV491937
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|211218550|gb|FL110185.1|FL110185
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|113702992|gb|EE680496.1|EE680496
EST:     AGGAAAGAGGATCAGGAGACAGACAAAGCATTTGGATGGGTTTTGGAAAT                         GTACGCATACGCTGTTGGTAGTGCACTGCACGGTGTGCACCATAGTTTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|211218551|gb|FL110186.1|FL110186
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTG
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTG
EST: gi|71760330|gb|DR958267.1|DR958267
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|60351853|gb|DN218826.1|DN218826
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
EST: gi|148981075|gb|EE027418.2|EE027418
EST:     ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT                         GTACGCATACGCTGTTGTTAGTGCACTGCACGGTGTGCACCATAGTCTCCA
genomic: ATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataa ... atatttgcagGTACGCATACGCTGTTGCTAGTGCACTGCACGGTGTGCACCATAGTCTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAATgttagtataaaattcttctctgcttctatttattctcttcaacatgtgctactcctattaatttctctttcccttttatatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA