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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctctcgagttatagtttgtattgccctgcattttaacaacgatcttgtttaccagttatgttctggttgttttttattacattgttattgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG

Basic information

species Zea mays
transcript GRMZM2G166345_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 10
-ttctctcgagttatagtttgtattgccctgcattttaacaacgatcttgtttaccagt---tatgttctggttgttttttattacattgttattgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG
 ||   | | ||| | ||  ||  ||| | |  | | || ||  |   ||||||  | |    |  ||   |||   ||  ||||| || |  || |  | |||||||||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || |||
atttgattgtgtt-tggt--gtcctgcaccgtttgtgaagaaaaaaaatgtttataactgtccacctttcagttcagttaaattac-ttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG
















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|18173735|gb|BM349123.1|BM349123
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|32913187|gb|CF017999.1|CF017999
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|31363989|gb|CD448344.1|CD448344
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|213173994|gb|FM188956.1|FM188956
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|32863847|gb|CF003529.1|CF003529
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|149110254|gb|EE294046.2|EE294046
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211207476|gb|FL411825.1|FL411825
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGGCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|56462002|gb|CK986300.1|CK986300
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|4874363|gb|AI673883.1|AI673883
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|4573130|gb|AI586779.1|AI586779
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|83279363|gb|DV943371.1|DV943371
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|91874366|gb|EB404323.1|EB404323
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|91873662|gb|EB403619.1|EB403619
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|33098108|gb|CF058068.1|CF058068
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211244774|gb|FL481676.1|FL481676
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|12972445|gb|BG267985.1|BG267985
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|4628469|gb|AI619343.1|AI619343
EST:     AAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: AAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211217164|gb|FL385248.1|FL385248
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGGCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|213173188|gb|FM191133.1|FM191133
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTGAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|32863787|gb|CF003469.1|CF003469
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|37381901|gb|CF627857.1|CF627857
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|32849223|gb|CD988904.1|CD988904
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|88756566|gb|DY540707.1|DY540707
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGTTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|24934254|gb|CA452472.1|CA452472
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|71758158|gb|DR956095.1|DR956095
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|33095762|gb|CF055756.1|CF055756
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|32944796|gb|CF049615.1|CF049615
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|93280898|gb|EB673162.1|EB673162
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211105793|gb|FL432184.1|FL432184
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|91053825|gb|EB164243.1|EB164243
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|5005650|gb|AI711712.1|AI711712
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211165085|gb|FL207333.1|FL207333
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|76286900|gb|DV026468.1|DV026468
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|17931240|gb|BM268200.1|BM268200
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|78112559|gb|DV530953.1|DV530953
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttaccagttatgttctggttgttttttattacattgttattgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG
                                          tattgat  putative branch site (score: 3)
                       ttgttttttattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctctcgagttatagtttgtattgccctgcattttaacaacgatcttgtttaccagttatgttctggttgttttttattacattgttattgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA