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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattaaaacacactgtttctgactgattttttaaaataagatctcacaactactgtgtttttgtacttatattttgccaatctattttcaaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC

Basic information

species Zea mays
transcript GRMZM2G083344_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 3'ss of exon 6
ggattaaaacacactgtttctgactgattttttaaaa-----taagatctcacaactactgtgtttttgtacttatattttgc-caatctattttcaaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC
      || || | | | | | |  || ||| ||        ||     || | ||| |||||  || ||| | || |   |   | ||| |||| |||| ||||||||| ||  | ||||| ||||||||||| ||||| ||||||||||| ||| ||||||||||||| || ||||| || ||||| |  || ||| | |||||
-----caagcatattatgttttag-gactttctagttgtctctatagcatctctacttctgtgcattggtaatcatttggagtatattctgttttgaaataatcagGTGTTTCAATGGCATCTCTCACTGAACTTTCATTCAATTGGACTGGTTTCGTTAATGCCATGATTTCTAATATCTCCTTCACATTACGGAGCGTTTATTC

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 6
ggattaaaacacactgtttctgactg-attttttaaaataagatctcacaactactgtgtttttgta-cttatattttgccaatctattttcaaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC
   |  ||| | | | | |   | || |  |  ||     | || |    | || |  ||   || | ||||   |   |     |||  || |||   ||||||| ||  | |||||  | || || |||||||| || |||   |||||||| | ||| ||||| ||||| ||||| ||||| |||||||||||||||||
--ttgtaaatagattatgtgacaatgcaggtaatatttgtacatttgcagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 6
ggattaaaacacactgtttctgactgattttttaaaataagatctcacaactactgtgttt-ttgtacttatattttgccaatcta--ttttcaaatgat-cagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC
                               | || |    |||  ||   | |  ||||| ||||      | |||       ||   ||| ||||| | |||||||  |  | || || || ||||| || ||||| || |||   || ||||| | ||| ||||| ||||| ||||||||||| |||||||||||||  ||
------------------------------gtaaacactcaatcaaactctttccatgtttcttgtgtcctaagtttattggattaacctttaaaatgttgcagGTGTTGCAATGGCTTCACTAACTGAGCTATCATTCAACTGGCTCGGTTTCATCAGTGCTATGATATCAAACATTTCTTTCACTTACCGAAGCATCTTCTC

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|71439302|gb|DR820352.1|DR820352
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGA
EST: gi|78087779|gb|DV516172.1|DV516172
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
EST: gi|148961156|gb|EE011865.2|EE011865
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
EST: gi|71768356|gb|DR966293.1|DR966293
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGNTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
EST: gi|91055754|gb|EB166172.1|EB166172
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
EST: gi|76930051|gb|DV172256.1|DV172256
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCA
EST: gi|149095075|gb|EE180680.2|EE180680
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
EST: gi|148962629|gb|EE013519.2|EE013519
EST:     ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTG                         GTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA
genomic: ACAACCAGTTCCATTGACACTCTGGCTGTCTCTTGTTCCAGTGGTGATTGgtatgtctta ... aaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaactactgtgtttttgtacttatattttgccaatctattttcaaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC
 atctcac  putative branch site (score: 3)
             tttttgtacttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattaaaacacactgtttctgactgattttttaaaataagatctcacaactactgtgtttttgtacttatattttgccaatctattttcaaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC

- - - aaacaca
- - - - - - - tgtttct
- - - - - - - - - - - actgatt
- - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttt