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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcacagtttagcaactcgtgaaattagtgtgtgcattttcttttcctttttcgaatgactttgtgaattttctatcattattgtag

Basic information

species Zea mays
transcript GRMZM2G425986_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G425986_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g10850.1 (Oryza sativa), 5'ss of exon 3
CGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttc-----acagtttagcaactcgtgaaattagtgtgtgcattttcttttcctttttcgaatgactttgtgaattttctatcattattgtag
 ||||| ||   ||| |||||||| || | | | || ||||| |||||||||||||||||||||||||| ||||| || ||||| || |||||||| |||||||| |     | | ||||        | |||| |   || |  |  || ||| | |  ||  |||| | ||| | |||  |   | | | |   
TGAAAAAGGCGAGTTCCCTTGCACAGCATCAACACTCCGTGAAGTTCGTGGCATTGGGGATTACACAGCAGGAGCCATTGCTTCCATAGCCTTCAATGAGgttgtgctccacataatttatatctgattcaaatcaccatgggtgtgatcctttacatactcacatgattatgtaactttcttgctaatgtag---
















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|76932963|gb|DV173258.1|DV173258
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|71323508|gb|DR798415.1|DR798415
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|71299540|gb|DR785778.1|DR785778
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|91874808|gb|EB404765.1|EB404765
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|76285023|gb|DV024591.1|DV024591
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTG
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTG
EST: gi|71441857|gb|DR822907.1|DR822907
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|78090907|gb|DV519281.1|DV519281
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|76926659|gb|DV170957.1|DV170957
EST:     CATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTNCA-CGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTA
genomic: CATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTT-CAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTA
EST: gi|71323967|gb|DR798666.1|DR798666
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|78103468|gb|DV521896.1|DV521896
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|74245470|gb|DT653384.1|DT653384
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|76920658|gb|DV168270.1|DV168270
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|71446168|gb|DR827218.1|DR827218
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
EST: gi|6865197|gb|AW360547.1|AW360547
EST:     GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAG                         GTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC
genomic: GCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcaca ... attattgtagGTTGTCCCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTTCAATTGCCTTCAACGAGgttgttcacagtttagcaactcgtgaaattagtgtgtgcattttcttttcctttttcgaatgactttgtgaattttctatcattattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA