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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatgctctccggctggtttatagtccattatctctctctctctctactaatggatatggtagtaacgggtaatgccctcaacttcttttgtctt...

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74580.1 (Oryza sativa), 5'ss of exon 2
ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatgctctccggctggt-ttatagtccattatctctctctctctc-tactaatggatatggtagtaacgggtaatgccctcaacttcttttgtctt
|||||||  | ||||| ||||||||||||||||||||  ||||||||||||| || || ||||| |||||||||||||| |||||||| || || ||||||||||  ||  | |  | | | |  | ||||  || |||  |   | | |  | |  ||   |     |||     || |    |   |    |  |  || 
ATGATGGATCACTTGGTCTGCTAAATGCTGTGTTGGAGGTTGACCCAAATCACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaat-ttgtgtgtccgttactttagtttataatccattcatgtttgattcacatattttcctcagttcaaagttacttaccagaaaaataattact-

upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g10180.2 (Oryza sativa), 5'ss of exon 3
ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaa------ttatgctctccggct-ggtttatagtccatt-atctctctctctc-tctactaatggatatggtagtaacgggtaatgccctcaacttcttttgtctt
|||||||  | ||||| ||||||||||||||| ||||  |||| |||||||| || || ||||| |||||||||||||| |||||||| || || ||||||||||      || |   |      |  | ||||| |||||| || | |   || | |||  |  |   |     ||| || |   |       || | ||        
ATGATGGATCACTTGGTCTGCTAAATGCTGTGCTGGAGGTTGAACCAAATCACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaaaagttgtatccgttactttagattataatccattcatgtttgattcacatctgttcctcagttcaa-agttactgaccagaaaaataattact--------
















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|148940996|gb|EC885847.2|EC885847
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|149079408|gb|EE168385.2|EE168385
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211247225|gb|FL156665.1|FL156665
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|148970832|gb|EE021601.2|EE021601
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|78080724|gb|DV509136.1|DV509136
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|71323581|gb|DR798459.1|DR798459
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211247229|gb|FL156669.1|FL156669
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|87155508|gb|DY400297.1|DY400297
EST:     CATTCTGAGGCTTACAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAATCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|78104565|gb|DV522983.1|DV522983
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211247228|gb|FL156668.1|FL156668
EST:     CATTCTGAGGCTTACAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAATCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|91875154|gb|EB405111.1|EB405111
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211247230|gb|FL156670.1|FL156670
EST:     CATTCTGAGGCTTACAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAATCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|149010182|gb|EE041997.2|EE041997
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|148960799|gb|EE011462.2|EE011462
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211245008|gb|FL156664.1|FL156664
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|149081738|gb|EE170891.2|EE170891
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211247231|gb|FL156671.1|FL156671
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|211247226|gb|FL156666.1|FL156666
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|26558848|gb|CA831083.1|CA831083
EST:     CATTCTGAGGCTTACAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAATCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|101391578|gb|EB817725.1|EB817725
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|22546040|gb|BU098361.1|BU098361
EST:     CATTCTGAGGCTTACAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAATCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|88758107|gb|DY542248.1|DY542248
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATTAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
EST: gi|148940390|gb|EC885183.2|EC885183
EST:     CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAG                         ATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG
genomic: CATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGGGTCTGCTTCAGTGGTGAAGGAATTATCCCAGCTTCTGCAGGCTCAAAAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 76

ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGGGTCTGCTTCAGTGGTGAAGGAATTATCCCAGCTTCTGCAGGCTCAAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGGGTCTGCTTCAGTGGTGAAGGAATTATCCCAGCTTCTGCAGGCTCAAAAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 218

ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatg ... taaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGGGTCTGCTTCAGTGGTGAAGGAATTATCCCAGCTTCTGCAGGCTCAAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTTGGAAATTGACCCAAATCATTCTGAGGCTTATAGGCAGCGTGCATCCGTGCTTCGGCATAAATGCAGgtaaattatgctctccggctggtttatagtccattatctctctctctctctactaatggatatggtagtaacgggtaatgccctcaacttcttttgtctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctctc