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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCAGTCAGCATCTTGTGTGGCTTTCGTCCTTATGATGTACAAGGAGGCTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctcctgaatcctttgcgttcaagtctctatgcctaggcagcaaaagcatctggtggggacatctgtttcgtgaatgcacgtatctcattgtct...

Basic information

species Zea mays
transcript GRMZM2G139374_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g58114.1 (Oryza sativa), 5'ss of exon 6
TGGTCAGTCAGCATCTTGTGTGGCTTTCGTCCTTATGATGTACAAGGAGGCTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctcctgaatcctt-tgcgttcaagtctctatgcctaggcagcaaaagcatctggtggggacatctgtttcgtgaatgcacgtatctcattgtct-
||| ||||| || ||||||||||||| ||||||||||||||||||||||||||||||||||||||| ||| |||||||||| ||||||||||||||||| |||||| ||| ||| | ||| || | |  |  ||  |   |  |    ||  || |||| | ||  |        ||    ||| |  ||| ||||   || 
TGGCCAGTCTGCTTCTTGTGTGGCTTACGTCCTTATGATGTACAAGGAGGCTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactcttgatttcttgtgtggtttatgcttaaattccggcttccatgag-atctag-ggtaattcagacatcaccgatggaactatatcatatgctc
















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|4609533|gb|AI600372.1|AI600372
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|6918323|gb|AW399853.1|AW399853
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|149069791|gb|EE158176.2|EE158176
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|12968323|gb|BG265269.1|BG265269
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|148965947|gb|EE016863.2|EE016863
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|6227276|gb|AW155875.1|AW155875
EST:     GAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: GAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|6601852|gb|AW256293.1|AW256293
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCCCA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|6637103|gb|AW261375.1|AW261375
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|13125900|gb|BG316575.1|BG316575
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|71311669|gb|DR792242.1|DR792242
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|50323956|gb|CO519082.1|CO519082
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|16377542|gb|BI991990.1|BI991990
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|71315242|gb|DR794239.1|DR794239
EST:     TGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: TGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|148946743|gb|EC892009.2|EC892009
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|211364275|gb|FL199172.1|FL199172
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|5791267|gb|AI978059.1|AI978059
EST:     ACTGAATTCCCA                         ATAAAAAATGCTTATATCCTCAACTTTTTTGAGGGCAACTCGACCCGACTT
genomic: ACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|76011881|gb|DT939051.1|DT939051
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|110532508|gb|EE036692.1|EE036692
EST:     GTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|110202366|gb|EC884263.1|EC884263
EST:     CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
EST: gi|74235210|gb|DT643124.1|DT643124
EST:     CTGGACTCTTTGACCCTATTTCCAGCTGTATTGAAGTTACTGAATTCACA                         ATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT
genomic: CTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctc ... tattttgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCAGTCAGCATCTTGTGTGGCTTTCGTCCTTATGATGTACAAGGAGGCTGGACTCTTTGACCCTATTACCAGCTCTATTGAAGTTACTGAATTCACAgtaagtgctcctgaatcctttgcgttcaagtctctatgcctaggcagcaaaagcatctggtggggacatctgtttcgtgaatgcacgtatctcattgtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG