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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttcccttactatacacccttgtcctgtttgccatggcaaaatttacaagacattcttgtag

Basic information

species Zea mays
transcript GRMZM2G330650_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330650_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g25390.2 (Oryza sativa), 5'ss of exon 6
CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttcccttactatac--acccttgtcc-tgtttgccatggcaaaatttacaagacat---tcttgtag
| |||||||| |||||||| || ||| | |||||  | ||||||   || || |||||||||||||| ||||||||||||||| |||  |  |||| ||  || ||||||  ||||       |  ||||||||| |||||   ||||||||
CTATGACAAACCAACAACTGATGGATGCTGGAAGAGAACAAATGACTCAGACTGATCAAGCTATTGACCGTTCAAAAATGgttgctttacgaactacactcactcttgtcaatgttctttcatgtcaaatttacaggacatctttcttgtag
















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|71774532|gb|DR972410.1|DR972410
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|60396385|gb|DN229254.1|DN229254
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|32866170|gb|CF005852.1|CF005852
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGTTTTTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|71774531|gb|DR972409.1|DR972409
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|50338100|gb|CO533226.1|CO533226
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|76286033|gb|DV025601.1|DV025601
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|21810005|gb|BQ668323.1|BQ668323
EST:     GCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|71442678|gb|DR823728.1|DR823728
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|60396054|gb|DN228924.1|DN228924
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|211141939|gb|FL417378.1|FL417378
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|211019324|gb|FL371811.1|FL371811
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTG
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTG
EST: gi|7135269|gb|AW498001.1|AW498001
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|78074383|gb|DV502817.1|DV502817
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|78122352|gb|DV540736.1|DV540736
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|32827094|gb|CD966772.1|CD966772
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTA
EST: gi|60337886|gb|DN204859.1|DN204859
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|110510919|gb|EE019261.1|EE019261
EST:     GAAGGACCCAAAGGGACCAACCAGATCAAGCTATTGAACGTTCAAAAAGG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|148961350|gb|EE012080.2|EE012080
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
EST: gi|76019098|gb|DT946268.1|DT946268
EST:     GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG                         GTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA
genomic: GAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttccc ... attcttgtagGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATGgttacttcccttactatacacccttgtcctgtttgccatggcaaaatttacaagacattcttgtag

- - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT