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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactatgtcatatatttgtggactgactagtagtttttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 19
aactatgtcatatatttgtggactgactagtagttt----ttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG
   | | |  | || | | |     || |||   |     |    |  |  |  |||  ||  | ||  | |   ||||||  ||| |  |   ||||||||||||||||||||||||| |||||||||| |||||||| |||   |||||||||||||| ||||||||||||||||   ||||| ||||   || ||||||||
---ttttttttttactcgagagagtacgagtgcctgaaaatagggagaaccgatgagtgatattttgcgtatttaatttattagttattgt-tgtgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG
















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|32933717|gb|CF038529.1|CF038529
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGTGACTCAG                         GGGAAAGGTGAATTTGCGATGGAGTA
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTA
EST: gi|32932818|gb|CF037630.1|CF037630
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGTGACTCAG                         GGGAAAGGTGAATTTACGATGGAGT
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGT
EST: gi|33093919|gb|CF053913.1|CF053913
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGTGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCT
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCT
EST: gi|69351603|gb|DR452190.1|DR452190
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG
                         tatttatctgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactatgtcatatatttgtggactgactagtagtttttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG