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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCTTGTGGCTGCACTGTCGTTGTCAAGCCATCAGAGTTCACACCTTTGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctctcaagttatctgcaactccacttatgttcaagtatttactattactagcgtagttcacatgcaatgcaaggatataaaaaaaatgtgtatt...

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 8
ATTGGCTTGTGGCTGCACTGTCGTTGTCAAGCCATCAGAGTTCACACCTTTGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctctcaagttatctgcaactccacttatgttcaagtatttactattactagcgtagttcacatgcaatgcaaggatataaaaaaaatgtgtatt-
 ||||| |||||||| ||||| |||||||||||||| |||||||||||| |||||||| | |||||||||||||||||||||||||| ||||||||||| |||||  |||| |||  |||   | | |  |    ||  |||||||| |    | |  ||   | |  |  || | |   |   || ||| | ||| | | 
TTTGGCCTGTGGCTGTACTGTTGTTGTCAAGCCATCGGAGTTCACACCTCTGACAGCATTAGCTGCAGCAGATCTTGCTCTTCAAGCGGGAATACCAGCGgtaatcatctcgagtcctctatcatttccatctaatttgagtatttatttcatcaaaagttactaat-tataaggtacaaaccaaagaaataggtgaactt

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G128114_T03 (Zea mays), 5'ss of exon 7
ATTGGCTTGTGGCTGCACTGTCGTTGTCAAGCCATCAGAGTTCACACCTTTGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctctcaagttatctgcaactccacttatgttcaagtatttactattactagcgtagttcac-atgcaatgcaaggatataaaaaaaatgtgtatt
 ||||| |||||||||||||| ||||||||||||||||||||||||||| ||||| || | |||||||||||||||||||||||||||||||||||||| |||||  |||| |||| |||   | |||  |    ||  |||||||| | |  | |  ||   | |  ||| | | |     |||||     |   | |  
TTTGGCCTGTGGCTGCACTGTTGTTGTCAAGCCATCAGAGTTCACACCTCTGACATCATTAGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCGgtaatcatctcgagttctctatcattcctgtctaattttagtatttattttgtcaaaagttactaattatgaagtacccct-tataatttggaatagcaga
















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|218496520|gb|FG947906.1|FG947906
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGC
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGC
EST: gi|218492832|gb|FG951181.1|FG951181
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCGA
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|88288968|gb|CI520298.1|CI520298
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|218492318|gb|FG946726.1|FG946726
EST:     AGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: AGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|88519470|gb|CI447124.1|CI447124
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|218490731|gb|FG966180.1|FG966180
EST:     CTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: CTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|66918914|gb|CX105762.1|CX105762
EST:     GCTCTTC-AGCT-GAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: GCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|58694576|gb|CK083263.1|CK083263
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
EST: gi|218491346|gb|FG955033.1|FG955033
EST:     TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCT                         GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA
genomic: TGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctct ... ttttatccagGGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGCTTGTGGCTGCACTGTCGTTGTCAAGCCATCAGAGTTCACACCTTTGACAGCACTTGCTGCAGCAGATCTTGCTCTTCAAGCTGGAATACCAGCTgtaattctctcaagttatctgcaactccacttatgttcaagtatttactattactagcgtagttcacatgcaatgcaaggatataaaaaaaatgtgtatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA