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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactcttgcttttcaaaggcagacagtttgtagttgttgcttttccagtttcaacactcaacataagatgctcattggttcttttgcag

Basic information

species Zea mays
transcript GRMZM2G034083_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034083_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 5'ss of exon 4
GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactcttgcttttcaaaggcagacagtttgtagttgttgcttttccagtttcaacactcaacataagatgctcattggttcttttgcag
|| || ||||| ||||||| |||||| |||| ||||| |||||||||||||||||   | ||    ||   |||   | | | | || | |||||| ||| | || |     |||||    |        |||| |  | | ||||
GTTCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgta---attcacagttgaaaaataaaaataatctggaattgttgttttccaagata----actcagttcat----tctattgatcttctggcag
















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|32848515|gb|CD988196.1|CD988196
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|13150055|gb|BG320377.1|BG320377
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|148986293|gb|EE030028.2|EE030028
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|149110454|gb|EE190425.2|EE190425
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|211020101|gb|FL063974.1|FL063974
EST:     TAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: TAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|149070778|gb|EE159189.2|EE159189
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|149000525|gb|EE037708.2|EE037708
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCCTTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|7238111|gb|AW573333.1|AW573333
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|31356652|gb|CD441009.1|CD441009
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|31353311|gb|CD437668.1|CD437668
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|13150060|gb|BG320382.1|BG320382
EST:     CGCACAAAGATAGGTGGTTTCATTWAGAGCTGTATTTTCTGTTTCCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CGCACAAAGATAGGTGGTTTCATT-AGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|211020099|gb|FL063972.1|FL063972
EST:     CGCNACAA-GATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTGGGATTTCTCATTTCTTGAGATGACCCCATTCAC-TTGGGTAAATGGT
genomic: CGC-ACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGG-TAAATGGT
EST: gi|148947869|gb|EC893362.2|EC893362
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAAT
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAAT
EST: gi|148958422|gb|EC904655.2|EC904655
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|31355046|gb|CD439403.1|CD439403
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|78103681|gb|DV522109.1|DV522109
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|148951643|gb|EC897387.2|EC897387
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTG
EST: gi|9566469|gb|BE475978.1|BE475978
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|67042517|gb|CO468772.1|CO468772
EST:     CCGCACAAAGATAGGTTGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|32859101|gb|CD998782.1|CD998782
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|148955951|gb|EC901669.2|EC901669
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|33104123|gb|CF064083.1|CF064083
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|149113031|gb|EE295802.2|EE295802
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|148935016|gb|EC879057.2|EC879057
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|37401585|gb|CF638160.1|CF638160
EST:     CCGCACAAAGATAGGTGG-TTCATTAGAGCTGTA-TTTCTG-TTTCCAAG                         AC-TGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
EST: gi|67016541|gb|CO445290.1|CO445290
EST:     CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG                         ACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG
genomic: CCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactc ... tcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactcttgcttttcaaaggcagacagtttgtagttgttgcttttccagtttcaacactcaacataagatgctcattggttcttttgcag

- - - - - - - - - - - - -  AGAGCT