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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaatgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctctttttctggaag

Basic information

species Zea mays
transcript GRMZM2G046587_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtatttta---atgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctcttttt--ctggaag
||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||| ||||||||    |||||| |||| |||||| | ||||||||||||  | |   |||| ||     |||    |      ||| |  | | ||  ||||||||||  |  | || |   |||  ||
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatggatgtgtgtgtgttttttaaaagaaaatat-acaaacctt-ctctaacattgcttctttttctctcctgatag

upper sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 4
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaatgt---atgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctctttttctggaag-------------------------
||||||||| || || |||||||| |||||||||||||| ||||| || || ||  ||||||| || | ||| ||  |||||||||| || || ||||||||| | | || |   || |    || |   |  | |     || |  | | || ||   || |       | || |  ||                          
TGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTCTAATGCAGgtagtgtcatttgacataccatcttaccacaatcatgatacattacatcttttttatttttctaattaaatcttataaaaattcatcaattcgccctctcgtgtag
















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|19351061|gb|BM895593.1|BM895593
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32849179|gb|CD988860.1|CD988860
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCGG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTTGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32924525|gb|CF029337.1|CF029337
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|18168735|gb|BM338575.1|BM338575
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|76016905|gb|DT944075.1|DT944075
EST:     CCCCCTGGATGTCCTCATATTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: CCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|149099848|gb|EE185900.2|EE185900
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|74244615|gb|DT652529.1|DT652529
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|74244614|gb|DT652528.1|DT652528
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|13126527|gb|BG317097.1|BG317097
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|211349013|gb|FL190902.1|FL190902
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|17931649|gb|BM268609.1|BM268609
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|60337363|gb|DN204336.1|DN204336
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32924252|gb|CF029064.1|CF029064
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|60348368|gb|DN215341.1|DN215341
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32831285|gb|CD970963.1|CD970963
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|13126526|gb|BG317096.1|BG317096
EST:     GGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|9732830|gb|BE511582.1|BE511582
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32851273|gb|CD990954.1|CD990954
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGAAG                       
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGC---AGgtattttaat ... tttctgga

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaatgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctctttttctggaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT