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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaccttaaggctgccattaagttctaacaacacgatgtttattttatttggatcctccatctctggaactaagtgagctttgttttgctttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCTGAGGTTCTCTTCCATAGGAAGAATACTGCTTCTATTAAAAC

Basic information

species Zea mays
transcript GRMZM2G020721_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 1
-taaccttaaggctgcc---attaagttctaacaacacgatgtttattttatttggatcctccatctctggaactaagtgagctttgttttgctttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCTGAGGTTCTCTTCCATAGGAAGAATACTGCTTCTATTAAAAC
   ||  ||  | || |    | |  ||||   || |  | | || | || |  || ||||| ||| ||||| || ||  ||||        ||||| |  ||||| |||||| ||||||| ||||| ||||||||| | || ||||| ||||| ||||||||||   ||||||||||| |||||||||||||| |
tctactatacagatgactgagtgatattcttctaatagtaggattttgttttgggggtcctcaatcactggatctgagatagctgg---caactttctg-acagGTCTCTGCTCTTCTGGGATTTCTTTGGGTTTTCACCGCCTGGGCATATGCGGAGGTTCTCTATTATAGGAAGAATGCTGCTTCTATTAAAGC
















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|148982690|gb|EE028501.2|EE028501
EST:     CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|148986950|gb|EE030765.2|EE030765
EST:     CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|71448158|gb|DR829208.1|DR829208
EST:     CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|211035508|gb|FL319750.1|FL319750
EST:     CTGCGGGCAGGCTCGCCATGGACTCCTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTTGCAGCATGGGCGTATGCC
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|211342552|gb|FL342004.1|FL342004
EST:     CTGCGGGCAGGCTCGCCATGGACTCCTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTTGCAGCATGGGCGTATGCC
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|211541629|gb|FL367734.1|FL367734
EST:     CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|91875375|gb|EB405332.1|EB405332
EST:     CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
EST: gi|211440830|gb|FL365412.1|FL365412
EST:     CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAG                         GTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT
genomic: CTGCGGGCAGGCTCGCCATGGACTCTTCGACCTCCGTCTCGCCCGGCCAGgtgagccgag ... ttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttggatcctccatctctggaactaagtgagctttgttttgctttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCTGAGGTTCTCTTCCATAGGAAGAATACTGCTTCTATTAAAAC
                                 ctttgttttgctttcc  CT-rich tract
                                  tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaccttaaggctgccattaagttctaacaacacgatgtttattttatttggatcctccatctctggaactaagtgagctttgttttgctttccgtgcagGTTTCTGCTATTCTGGGCTTTCTGTGGGTTTTCGCAGCATGGGCGTATGCTGAGGTTCTCTTCCATAGGAAGAATACTGCTTCTATTAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA