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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgtaattgatgtaatagtaataccaaataacatactgattatattgtgcactttctgatctggttgctattcttattgctggttgatacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCACGATGATTTA

Basic information

species Zea mays
transcript GRMZM2G047223_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g31840.1 (Oryza sativa), 3'ss of exon 6
----aatctgtaattgatgtaatagtaataccaaataacatactgattatattg-tgcactttctgatctggttgctattcttattgc-tggttgatacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCACGATGATTTA
    ||  || ||||||  | ||   | | |||       ||||| |  | ||| ||||   |   |           |  ||| ||  |  ||| || ||| ||||| ||||||||||||||||||||||||||||||||||||||| | || || ||||| || 
ttgtaaagtgcaattgaactcatttaatttcca-----tctactggtcttcttgatgcaagattaaaaaaaaaaatactgattactgtgtcattgttatcta-cagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCATGATGAATTG
















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|71771757|gb|DR969694.1|DR969694
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|89247292|gb|DY619078.1|DY619078
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|60347298|gb|DN214271.1|DN214271
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|61118400|gb|DN559361.1|DN559361
EST:     CCTTCCCATTCCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|91874335|gb|EB404292.1|EB404292
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|78118514|gb|DV536898.1|DV536898
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|78117554|gb|DV535941.1|DV535941
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|78113904|gb|DV532293.1|DV532293
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
EST: gi|211528671|gb|FL445665.1|FL445665
EST:     CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAG                         GGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC
genomic: CCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatct ... tacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtgcactttctgatctggttgctattcttattgctggttgatacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCACGATGATTTA
                          tattcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgtaattgatgtaatagtaataccaaataacatactgattatattgtgcactttctgatctggttgctattcttattgctggttgatacctaacagGGTATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGACTCTGTCACGATGATTTA

- - - - - tgatgta
- - - - - - - - - - - - - ccaaataa
- - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgctg