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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACGGTGGGGCCGCGAAGGGGAGGAGCAGGGGCGGGGCCGTCCCCGCTGGGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagctgggtggaattgtggctccctaacttggtggatttgtggctccctgttaggtttggtgttggttacagttggcattcgcgaaatggctctg...

Basic information

species Zea mays
transcript GRMZM2G081188_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081188_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 5'ss of exon 1
GGACGGTGGGGCCGCGAAGGGGAGGAGCAGGGGCGGGGCCGTCCCCGCTGGGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagca-gctggg---tggaattgtggctccctaa-cttggtggatttgtggctccctgttaggtttg-gtgttggttacagttggcattcgcgaaatggctctg
| | ||   ||    |  | || |||| || |||| |||||| |||   |||||| |||| |||||||||||||||||||||||||| ||||| ||||||||||||  |||| |   || |    ||   || |   ||  |  ||||  ||  |  |   | | | || |   ||| | |  ||     |    |  ||      
GAAAGGGAAGGGGAGGGGGAGGGGGAGGAGCGGCGCGGCCGTTCCCATGGGGGCCTCCGTTAGGGCCGTGCCGCTGCAGTCGCCGCTGCCGCCCGCCGAGgtgagcttgctgtgaattgtacacatgctgccatgttctctgctgattactgtttgtccaatggctctgcgctgtgggttcgatttagggtgattagctg------
















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|211294773|gb|FL058751.1|FL058751
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211292640|gb|FL058746.1|FL058746
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211299060|gb|FL058784.1|FL058784
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|148945695|gb|EC890968.2|EC890968
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211292628|gb|FL058734.1|FL058734
EST:     GGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCCGAG                         -AAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGA
genomic: GGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCC-GAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGA
EST: gi|148953714|gb|EC899078.2|EC899078
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211288358|gb|FL058718.1|FL058718
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211290491|gb|FL058723.1|FL058723
EST:     GGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGNAG                         -AAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGA
genomic: GGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCG-AGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGA
EST: gi|211294783|gb|FL058761.1|FL058761
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211290496|gb|FL058728.1|FL058728
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211296915|gb|FL058767.1|FL058767
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAANGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|149076159|gb|EE164750.2|EE164750
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211292635|gb|FL058741.1|FL058741
EST:     GGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCCGCCTGC-GAG                         GAAATAATGNCATTCATAAGATCATATGTGGTGCCTGAAAGGGTT-CCAGA
genomic: GGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCC-GCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAA-GGGTTTCCAGA
EST: gi|211294782|gb|FL058760.1|FL058760
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211296923|gb|FL058775.1|FL058775
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGGAGGGGTTTCCAGA
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGG-TTTCCAGA
EST: gi|211290489|gb|FL058721.1|FL058721
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGGCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGGTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211299063|gb|FL058787.1|FL058787
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211290499|gb|FL058731.1|FL058731
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211294774|gb|FL058752.1|FL058752
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211290497|gb|FL058729.1|FL058729
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGNTGCCTGAAGGGTTTCCAGA
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGG-TGCCTGAAGGGTTTCCAGA
EST: gi|211292631|gb|FL058737.1|FL058737
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGGAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211294779|gb|FL058757.1|FL058757
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|149110553|gb|EE190479.2|EE190479
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|148958478|gb|EC904716.2|EC904716
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGTCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|148966241|gb|EE017202.2|EE017202
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211288350|gb|FL058710.1|FL058710
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211296919|gb|FL058771.1|FL058771
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211301191|gb|FL058791.1|FL058791
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTNCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211288352|gb|FL058712.1|FL058712
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGGAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211517299|gb|FK997845.1|FK997845
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211296912|gb|FL058764.1|FL058764
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|211290488|gb|FL058720.1|FL058720
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
EST: gi|149012213|gb|EE042512.2|EE042512
EST:     GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAG                         GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC
genomic: GGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagct ... atggttgcagGAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACGGTGGGGCCGCGAAGGGGAGGAGCAGGGGCGGGGCCGTCCCCGCTGGGGCCGCCGTCAGGGCCGTGCCGCTGCAGTCGCCGCTTCCGCCTGCCGAGgtgagcagctgggtggaattgtggctccctaacttggtggatttgtggctccctgttaggtttggtgttggttacagttggcattcgcgaaatggctctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG