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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaacacgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag

Basic information

species Zea mays
transcript GRMZM2G164265_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
CAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaacacgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag
   ||  ||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || |||||  |||||||||| ||||| ||||| |||   || |||||| || || ||||||| |      | || ||| |    |  |||||  ||  |     || |  |    | || ||  |  |  ||||                                            
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattaca-tcaaagaactagatgatataaagcatgatcgacc---tgcatttgtt----tagtctaggtacttgcttttct-tggatgcaaacaatagtaatt--tgaa--------------------------------------------

upper sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 12
CAAATCT---AGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaacacgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag
   ||||   ||||||||| |||||||| ||||| ||  |||| ||||| || ||  |||| ||||| ||||| ||||||||| | || ||||||||||||||||| |||  |       || |    ||     || || |   ||  | |   |||| |  | | | |   | ||   |    | |     ||||    || |   | ||||                                            
---ATCTGGAAGAAGATGAGCAACCTAAGAAGAAAGTGCGATTGGGGAGTCCTGCTACTCAGTGGATATCAGTGTATAATGCTCGCCGTCCCATGAAGCAGAGgtaattaatac------atcattctctgtctagcttgtt--cttaataatg-ttgcagattatttgttaaatcataaacttttcttgctttgatg--caaaagcagttgaa--------------------------------------------

upper sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 12
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 11
CAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaaca-cgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag
 | |    || ||||| ||||| || |||||| || | ||||| |  || ||  ||||||||||| | |||||||||||| ||||||| |||||||||||||| || |||      ||  ||  | ||||| |  ||  |||  | |   |  ||||||    || |||||  |  || | ||||   |  ||        |  |  ||                                               
AAGAGGATGAGGATGACCAACCGAAGAAGAAGATTCGCTTAGGAATGCCTGCTACTCAATGGATTACCGTTTATAATGCTCGGCGACCTATGAAGCAGAGgtaattgcaaa-----aacaagtcgttacaacgattg--agtcagatatta--tgctgcgaggct-tagtattagtgtcgtcctgcctatttgggttgcttggggacata----------------------------------------------

upper sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 12
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 11
CAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaacacgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag
 | |    || ||||| |||||||| || ||| |  | ||||| |  || ||  ||||||||||| | ||||| || ||| ||||||| |||||||||||||||   |  |       | || |      |   ||| | || || |     ||||| || ||    |  | | ||  | | |||    ||  ||  |    | |||     | || ||                                    
AAGAAGATGAGGATGACCAACCTAAGAAAAAGATCCGGTTAGGAATGCCTGCAACTCAATGGATTACCGTTTACAACGCTCGGCGACCAATGAAGCAGAGgtatg-gcggt------gtgagctttcgtcattgatg-tggtgtgat----gttgct-cagttaggcatcagcccg--gtcatgtctgtatcgtcgat----tttgactctgtcttcct------------------------------------

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|149102515|gb|EE287878.2|EE287878
EST:     CGGCTCAATGGA-TTCAGGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: CGGCTCAATGGATTTCA-GTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|32912903|gb|CF017715.1|CF017715
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|148974692|gb|EE025499.2|EE025499
EST:     GCGGCTCAATGGATCTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|71430774|gb|DR811824.1|DR811824
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|149031683|gb|EE154868.2|EE154868
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|211391059|gb|FL093738.1|FL093738
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|78113586|gb|DV531977.1|DV531977
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|149098314|gb|EE184284.2|EE184284
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|148937186|gb|EC881367.2|EC881367
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|71300241|gb|DR786191.1|DR786191
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|148950556|gb|EC896133.2|EC896133
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|71764976|gb|DR962913.1|DR962913
EST:     AATGGATTTCAGTTTATAATGTTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGTTGACTCAAGGGTAAGTCAACATATAGAAAAGGG
genomic: AATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAA-GG
EST: gi|37423723|gb|CF649590.1|CF649590
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|32913238|gb|CF018050.1|CF018050
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|32855731|gb|CD995412.1|CD995412
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
EST: gi|148950415|gb|EC895982.2|EC895982
EST:     GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAG                         GTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG
genomic: GCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaa ... tgtttcttagGTACCATTACAATGTGGCTGACTCAAGGCTAAGTCAACATATAGAAAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaacacgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC