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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn...

Basic information

species Zea mays
transcript GRMZM2G032505_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 4
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn------------------------------------------------------------------------------------
 || ||| ||||||||||||| ||||||||||| ||||||||||| ||||||||||| ||||| || || || ||||| ||||| |||||||||||||||                                                                                                                                                                                        
GGACACACTGCCATCAGAGTATGATTCACGAGTAAAGGCAATGGAGGTGGATGAAAAACCCACAGAGGACTACAATGATATTGGAGGTCTTGAAAAGCAGgtacattgcttaataaatgttgaaagttcagtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatag

upper sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
 |||||  |||| || ||||| |||||  |||| ||||| |||||||| ||||||||||| || || ||||| ||||||||||| ||  | || ||||||                                                                                                    
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag--------------

upper sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn-----------
 ||| |  |||| || ||||| ||||||||||| ||||| |||||||| ||||||||||| || || || || ||||||||||| ||| | || ||||||                                                                                                               
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag

upper sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
 ||||| ||||| || ||||| |||||  |||| ||||| |||||||| ||||||||||| || || || || ||||||||||| ||  | || ||||||                                                                                                    
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagttaatgcaatctctcaggtcatttcaataacttggtcttcctcaacag---

upper sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 5'ss of exon 5
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn-----
 || ||  | || || || || ||||| ||||| ||||| |||||||| ||||||||||| ||||||||||| ||||||||||||||||| || ||||||                                                                                                         
GGACACTCTTCCGTCTGAATATGATTCTCGAGTAAAGGCTATGGAAGTCGATGAAAAGCCAACTGAAGATTACAATGACATTGGGGGTCTGGAGAAGCAGgtgaattttggactgaacatatttcatagagggattccccagggttcttgttacatgccagattcttcgtagttgtttcttttgataaatgcacttttgtaacag

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|78179300|gb|DV549673.1|DV549673
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|47961752|gb|CN844461.1|CN844461
EST:     GTGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149062853|gb|EE157572.2|EE157572
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|60346168|gb|DN213141.1|DN213141
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAAAGGCAATTGTACTGCCCATGACACATAAAGACCG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCG
EST: gi|148979721|gb|EE026794.2|EE026794
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149077127|gb|EE165787.2|EE165787
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|22133556|gb|BQ833772.1|BQ833772
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|21809844|gb|BQ668162.1|BQ668162
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|32823651|gb|CD963373.1|CD963373
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149109720|gb|EE293507.2|EE293507
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|211138446|gb|FL259171.1|FL259171
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTTCA-GAGCTTTGTAGAG-CAATTGTACTGCC
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATT-CAAGAGCTT-GTAGAGGCAATTGTACTGCC
EST: gi|116820064|gb|EC863249.1|EC863249
EST:     ATGAAAAGCCCACTGAAGATTATAATGGCATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149100563|gb|EE186648.2|EE186648
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149096589|gb|EE182348.2|EE182348
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149085416|gb|EE174922.2|EE174922
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|74241694|gb|DT649608.1|DT649608
EST:     ATGANAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|148951330|gb|EC897040.2|EC897040
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149101527|gb|EE187650.2|EE187650
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA