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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTACAGTGACTTGAATGTTGACTACCTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcatcctcattcttggatccttcatccttatacttaaatcttcttttattatatatctgttactgttccagttattcttttacttacttaagctagtactagtaggcttcaatttgttgtgtctgttcaccctcttgacgaatatctaacattactttccttacatttag

Basic information

species Zea mays
transcript GRMZM5G896082_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896082_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 4
GTGTACAGTGACTTGAATGTTGACTACCTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcatc----ctcattcttggatccttcatccttatacttaaatcttct---tttattatatatctgttactgttccagtta---ttcttttacttacttaagctagtactagtaggcttcaatttgt--tgtgtctg--ttcaccctcttgacgaatatctaacattactttccttacatttag
||||||||||| ||||  ||||||||||||||||||||||| |||||||||||||| || ||  | ||||| ||||||||||||| |     |||| |||||  ||||||  |  ||||| ||  |  | |    | | |||    |||| | | | ||  |||   | | ||  | |  |     | | ||| || |     ||||  |  | | || |  || ||     |     |  |||||  |   ||| | | |||||||
GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACTgtgagttcttttcatctcactcttgcttccttc--caatatacctagctagtatgaaataaatattggactgtcagtataccttttactgtccattgtcctggtgggatttgaactggttgcgacgaattcatcctttatcagactttacttatgtttgtcacctctaatttcgatttgcatgcatttag
















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|149051802|gb|EE155929.2|EE155929
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCAACGTAGCTCTGGGACT                         GTTCCTTTTCATTGATGAATTGACTGGTTT
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTT
EST: gi|32849671|gb|CD989352.1|CD989352
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTATTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|149070758|gb|EE159171.2|EE159171
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGCT
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGCT
EST: gi|71325794|gb|DR799576.1|DR799576
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|148959398|gb|EC905432.2|EC905432
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|78092904|gb|DV521278.1|DV521278
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|71449206|gb|DR830256.1|DR830256
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|74239749|gb|DT647663.1|DT647663
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|71435282|gb|DR816332.1|DR816332
EST:     TAAAGATGTTCCTCCTAAATTGT-CCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTG
genomic: TAAAGATGTTCCTCCTAAAT-GTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTG
EST: gi|93014353|gb|EB639873.1|EB639873
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|71773101|gb|DR971019.1|DR971019
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|149097127|gb|EE182939.2|EE182939
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|149111107|gb|EE294603.2|EE294603
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTT
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTT
EST: gi|149058763|gb|EE156781.2|EE156781
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|71322554|gb|DR797954.1|DR797954
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCATCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|71775245|gb|DR973123.1|DR973123
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|71763483|gb|DR961420.1|DR961420
EST:     CTAAAGATGTTCTTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|13516143|gb|BG518419.1|BG518419
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|149011246|gb|EE042332.2|EE042332
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTT-CATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|78107802|gb|DV526220.1|DV526220
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
EST: gi|148949267|gb|EC894710.2|EC894710
EST:     CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT                         GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG
genomic: CTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcat ... ttacatttagGTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTACAGTGACTTGAATGTTGACTACCTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACTgtgagttcatcctcattcttggatccttcatccttatacttaaatcttcttttattatatatctgttactgttccagttattcttttacttacttaagctagtactagtaggcttcaatttgttgtgtctgttcaccctcttgacgaatatctaacattactttccttacatttag

- - - - - - - - - - - - - - - AAGATG