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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTTCATGCACTGGTTTATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaattgctatttgtaatgaaaatactttggtcacttgacattttttatatcttcctttttgatattcttctgattttttaatttgtcactggata...

Basic information

species Zea mays
transcript GRMZM2G070284_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070284_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G39100.1 (Glycine max), 5'ss of exon 5
GGCCTTCATGCACTGGTTTATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaattgctatttgtaatgaaaatactttggtcacttgacattttttatatcttcctttttgatattcttctgattttttaatttgtcactggata--
|| || |||||  |||||||||| ||  || | ||| ||||||| |||||||||||| |||||||||||||| ||  || | || | ||||     | | |   ||| |  ||||    | ||  ||    || | | ||  | |  |||| |  ||   || |   |   
GGACTACATGCTTTGGTTTATGATATGAATTCAGCAAATGAAACATGGGAGTGGGTTAATCTTAAAGAGgtaaaattttacaatat-taatattcttccgtctatcattc-acatacaatctagttttagcttggttctttcttttcttttctttttaagcaatattttcc
















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|31363341|gb|CD447698.1|CD447698
EST:     TGACATCGATACGGCAGATG-AACCTGGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: TGACATCGATACGGCAGATGAAACCT-GGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
EST: gi|20802968|gb|BQ294018.1|BQ294018
EST:     ATGACATCGATACGGAAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
EST: gi|91878730|gb|EB408687.1|EB408687
EST:     TGACATCGATACGGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: TGACATCGATAC-GGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
EST: gi|32850267|gb|CD989948.1|CD989948
EST:     ATGACATCGATACGGAAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
EST: gi|76930208|gb|DV172294.1|DV172294
EST:     ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
EST: gi|21432223|gb|BQ547713.1|BQ547713
EST:     ATGACATCGATACGGAAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
EST: gi|211378805|gb|FL247494.1|FL247494
EST:     ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAG                         ATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT
genomic: ATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaatt ... ttgagtacagATGGGACCTGAAGACATAAGATGGCAAGAGGATGACTCTGGGATAGACCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCTTCATGCACTGGTTTATGACATCGATACGGCAGATGAAACCTGGGAGTGGGTTGATCTTAAAGAGgtagaaaattgctatttgtaatgaaaatactttggtcacttgacattttttatatcttcctttttgatattcttctgattttttaatttgtcactggata

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