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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgttgttccctgtttatgttcatgttaaactctcaattccaacatgttgtttgttttccag

Basic information

species Zea mays
transcript GRMZM2G124965_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124965_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 5'ss of exon 2
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagct--tctgt-tgttccctg------------tttatgtt-catgttaaactct-caattccaacatgttgtttgttttccag
|| ||| |||||||| ||||||||||||||||||||||| | ||||  |||||| |||||||| || |||||| | |  ||| | ||||||||||||||||| || | |  |   |||  | |  | ||               |  || ||| || ||   |  |||| |||||||||| |||||||  ||
TGATGAATTTCGTCTGAAGTGGGATCCCATGCTTGCATATTTCAAAATTTTGGAGGAGTTCCCCCAAAATGGAACTATGATTATTCACTGGATAAAAAAGgtatgacaacttgacctgcatatctcttgacaagcatatcccccaaattacatattgaatcatgtaatttcaacatgttgcttgttttgtag

upper sequence: GRMZM2G124965_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0020g04870.t01 (Vitis vinifera), 5'ss of exon 3
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgtt--------gttccctgtttatgttcatgttaaactctcaattccaacatgttg--tttgttttccag-----------------------
|| ||| ||| | |  || ||||| || |||||||| || |  |||   ||||| || |||||||| |  |   |||  |||||||||||||||||||||||||||  | | |    |         |   ||  | ||||      | ||  ||   | |||  || |||  ||  | |  ||                        
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag
















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|149083327|gb|EE172619.2|EE172619
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTTGGGAG-ACGCATAT
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTT-GG-AGGACGCATAT
EST: gi|32940863|gb|CF045682.1|CF045682
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|71769408|gb|DR967345.1|DR967345
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCC-ATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|149111705|gb|EE190850.2|EE190850
EST:     TGGATGAGTTCCCTCAGAATGGAGCACCAATTGTCCACTGGATAAAAAAG                         T-CCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGGAGGACGCA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGG-AGGACGCA
EST: gi|91055562|gb|EB165980.1|EB165980
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCA
EST: gi|211387106|gb|FL377395.1|FL377395
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|5915166|gb|AW052807.1|AW052807
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|211156664|gb|FL403854.1|FL403854
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|71437018|gb|DR818068.1|DR818068
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAAATGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATA
EST: gi|211217740|gb|FL411413.1|FL411413
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|94472323|gb|EB701281.1|EB701281
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAA-G                         TTCCCATTCTTTTGCAGTGACCGTGAATA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATA
EST: gi|32942520|gb|CF047339.1|CF047339
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|31354728|gb|CD439085.1|CD439085
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCCATTCTTTTGCAGTGACCGTGAATACAT
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCC-ATTCTTTTGCAGTGACCGTGAATACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgttgttccctgtttatgttcatgttaaactctcaattccaacatgttgtttgttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA