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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttccttttcctcctctatctctcccaccgccttcctcatcttagggttagttaatgctttacagatggggatgcctgacagatggattacagac...

Basic information

species Zea mays
transcript GRMZM5G868757_T07
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T07 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 1
CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttccttttcctcctctatctctccc-----accgccttcctcatcttag---ggttagttaatgctttacagatggggatgcc-tgacagatggattacagac
| |||||  |||||||  ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||| | |||||||  | ||| ||||||  |  ||   |||||| ||  | ||| |     | ||||||| |  |||| |   |||||| |  ||     |   |  ||||  |    || |            
CGCCGACCCGTACGCCGACCTCGCCGACCTCTACCAGCGGAAGCTCTGGCACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAGCTCCCTGCCGCGCAGgtttcccaccacctcctcccctcaccctctcttgcaagcgccttcttgttcttggttaggttagctgctgtcccccccgtacggatctcgccgcaaaccc---------

upper sequence: GRMZM5G868757_T07 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 1
CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttccttttcctcctctatctctcccac-cgccttcctcatcttagggttagttaatgctttacagatg-----gggatgcctgacagatg-gattacagac
| |||||   ||||||  ||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||| ||| | || ||||  | ||| |||||  ||   ||||||| | ||   ||||   |  |||||     |  ||||    | |     |  ||| |||      |  |  |||  | |  | | ||  ||  
CGCCGACGCCTACGCCGACCTCGCCGACCTCTACCAGCGCAAGCTCTGGCACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgca--cttttccccttc---ctcttagatgcgcctcttctaggttag--ccactgccccccatacggatctcgccgcaaaccctacccgccgcgtttgtaggt

upper sequence: GRMZM5G868757_T07 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 1
CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttc-gcttccttttcctcctctatctctcccaccgccttcctcatcttagggttagttaatgctttacagatggggatgcctgacagatggattacagac
|||||| ||||||   || || || || || ||||||  |||||| |||||||||||||| ||||||||||| || ||  |    |||   |||   ||||||| |||    ||||||   |  || |    |  |   |  |  | | |   ||| |    ||||      ||        ||    |  ||||      
CTCCGATTGGTACAATTCGCTGGCGGATCTGTACCAGAAGAAGCTCTGGCACCAGCTCACTCTCAAGCTCGAGCAGTTTGTGGCTCTCGCCGTCTTCCAGgttcagctcttctttccttaccactcgcaattattgttgttgttctataactattattactggcttcgtgtttgctttgttttgtttcaacgattgttag-

upper sequence: GRMZM5G868757_T07 (Zea mays), 5'ss of exon 1
lower sequence: PP1S66_117V6.1 (Physcomitrella patens), 5'ss of exon 1
CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgt-tcgcttccttttcctcctctatctctcccaccgccttcctcatcttagggttag-ttaatgctttacag-atggggatgcctgacagatggattacagac
| |||| |||||||||  | | ||||| || |||||||| ||||| |||||||||||||| |  ||||||||||| ||| |   ||||   ||    ||||| | |  |  ||   |         |    | | |   |  || | ||   |  || ||  || | |  ||  || ||  |   |||    || |  |    
CGCCGAGTGGTACGCCAGCATGGCCGATCTGTACCAGCGCAAGCTTTGGCACCAGCTCACGCAGAAGCTCGACCAGTTCGTGGCGCTCACCGTGTTCCAGgtattggatgtttccaccttgtcggtttaatcgctgtggttttcgtgttcaagcgaggttgttgttgttgagcgtgcggtggttcgacttgggggtggct---

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|211319212|gb|FL155860.1|FL155860
EST:     ACCAGCTCACCCTCAASCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|149078129|gb|EE166878.2|EE166878
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211132128|gb|FL064538.1|FL064538
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCAACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211132126|gb|FL064536.1|FL064536
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148986083|gb|EE029890.2|EE029890
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148965470|gb|EE016279.2|EE016279
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211132131|gb|FL064541.1|FL064541
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATTCATTCAGCTCT
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTAT-CATTCAGCTCT
EST: gi|211277769|gb|FL330867.1|FL330867
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211099199|gb|FL356879.1|FL356879
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|21891735|gb|BQ744948.1|BQ744948
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148930110|gb|EC872431.2|EC872431
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148948407|gb|EC893924.2|EC893924
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319213|gb|FL155861.1|FL155861
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148982851|gb|EE028701.2|EE028701
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211131207|gb|FL064532.1|FL064532
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTG
EST: gi|14529417|gb|BI096550.1|BI096550
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCACACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319209|gb|FL155857.1|FL155857
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|26557995|gb|CA830230.1|CA830230
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211540331|gb|FL320589.1|FL320589
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|101383033|gb|EB813569.1|EB813569
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211132130|gb|FL064540.1|FL064540
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGNAGACACTATCATTCAGCTCTACAACAATTTCATTGTCAACTTTGA
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGG-AGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGA
EST: gi|211132124|gb|FL064534.1|FL064534
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGTAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGA
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGG-AGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGA
EST: gi|22521302|gb|BU080113.1|BU080113
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319208|gb|FL155856.1|FL155856
EST:     ACCAGCTCACCCTCAAGCT-GACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|149069680|gb|EE158063.2|EE158063
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|9731352|gb|BE510104.1|BE510104
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|5268656|gb|AI770620.1|AI770620
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|149081820|gb|EE170979.2|EE170979
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|16927387|gb|BM080456.1|BM080456
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttccttttcctcctctatctctcccaccgccttcctcatcttagggttagttaatgctttacagatggggatgcctgacagatggattacagac

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC