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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttcattttacctcattatctttgtttttccttctcttaattgtttttttggatttcttgtgcaaaatactgtatacacatgttttcctgagctattggtagttatgaagAAGCGAAAGCAAAGGGAACAGAGAATTTTGACAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGCGACAGGAAAATTCAGAGGGCCCTGAA

Basic information

species Zea mays
transcript GRMZM2G118014_T06
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 2
gtatccttcattttacctcattatctttgtttttccttctcttaattgtttttttggatttcttgtgcaaaatactgtatacacatgttttcctgagctattggtagttatgaagAAGCGAAAGCAAAGGGAACAGAGAATTTTGACAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGCGACAGGAAAATTCAGAGGGCCCTGAA
||||||||    |||    |    |||  | ||||    | | || | ||        | |  |||  | | ||  ||   |   ||  ||||||| || || | |||||||||||||  || ||||| |||||||| |||| ||| || ||||||||||| |||||||| |||||||| ||||||||||| |||||||||||||||        
gtatcctttgacttatggaaca--cttcatctttctccttttaaaatattccgc--actctactgtatagagtatagtggtctt-tgccttcctgaactgttcgcagTTATGAAGAAGTAAAGGCAAAAGGAACAGAAAATTATGATAGGGAACTCGAGGAAATGATAGACAGGCTCATCGTGGAGTGCGAGAGGAAAATTCAGAGG--------
















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|76020071|gb|DT947241.1|DT947241
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|76020071|gb|DT947241.1|DT947241
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|211387620|gb|FL172483.1|FL172483
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211387620|gb|FL172483.1|FL172483
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211387620|gb|FL172483.1|FL172483
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|87153157|gb|DY397946.1|DY397946
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|87153157|gb|DY397946.1|DY397946
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|87153157|gb|DY397946.1|DY397946
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|22491280|gb|BU051203.1|BU051203
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGAGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|22491280|gb|BU051203.1|BU051203
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGAGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|22491280|gb|BU051203.1|BU051203
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGAGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|149079348|gb|EE168324.2|EE168324
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|149079348|gb|EE168324.2|EE168324
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|211384990|gb|FL172469.1|FL172469
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384990|gb|FL172469.1|FL172469
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384990|gb|FL172469.1|FL172469
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|76284913|gb|DV024481.1|DV024481
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|76284913|gb|DV024481.1|DV024481
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|211384994|gb|FL172473.1|FL172473
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384994|gb|FL172473.1|FL172473
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384994|gb|FL172473.1|FL172473
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211390254|gb|FL172494.1|FL172494
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211390254|gb|FL172494.1|FL172494
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211390254|gb|FL172494.1|FL172494
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|87152221|gb|DY397010.1|DY397010
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|87152221|gb|DY397010.1|DY397010
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|87152221|gb|DY397010.1|DY397010
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|71445995|gb|DR827045.1|DR827045
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|71445995|gb|DR827045.1|DR827045
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGATTATGAA                   
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGG--A-A--A-G-Agtatccttca ... agtt
EST: gi|211063251|gb|FL401238.1|FL401238
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         AAGCGAAAGCAAAGGGAACAGAGAATTTTGACAGAGAACTCGAGGATATGA
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaagAAGCGAAAGCAAAGGGAACAGAGAATTTTGACAGAGAACTCGAGGATATGA
EST: gi|211387625|gb|FL172488.1|FL172488
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211387625|gb|FL172488.1|FL172488
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211387625|gb|FL172488.1|FL172488
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211390250|gb|FL172490.1|FL172490
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211390250|gb|FL172490.1|FL172490
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211390250|gb|FL172490.1|FL172490
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384992|gb|FL172471.1|FL172471
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384992|gb|FL172471.1|FL172471
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-
EST: gi|211384992|gb|FL172471.1|FL172471
EST:     ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA                         T
genomic: ATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGAgtatccttca ... agttatgaag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtgcaaaatactgtatacacatgttttcctgagctattggtagttatgaagAAGCGAAAGCAAAGGGAACAGAGAATTTTGACAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGCGACAGGAAAATTCAGAGGGCCCTGAA
 ttcctgagc  putative branch site 
        aaaatact  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttcattttacctcattatctttgtttttccttctcttaattgtttttttggatttcttgtgcaaaatactgtatacacatgttttcctgagctattggtagttatgaagAAGCGAAAGCAAAGGGAACAGAGAATTTTGACAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGCGACAGGAAAATTCAGAGGGCCCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG