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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagcgtgatctcgactctggatctctatttcactcaccgttagacatgggcttgttcgcgtgttccgaatcctgatttttggtgcccaattgctgtttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 2
gtgagagcgtgatctcgactctggatctctatttcactcaccgttagacatg-ggcttgttcgcgtgttccgaatcctgatttttggtgcccaattgctgtttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG
        ||||| | |   | |||||              ||    | | | |||  | ||||  |  | |    |||||| || |||     |||    |   | ||||| |||||| ||||||| ||||| || || || ||||||||||||||||||||||| ||||||||||||||||||||||||||||||
--------gtgattttg--ccgggatccgatcgctggatctcgccgtatacgtggcccgatcgctcgacctgg--tctgattgttcgtgggtgtttgtgtgtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG
















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|32829264|gb|CD968942.1|CD968942
EST:     CGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGTGGGCTTCATCGGCTCGTAC
genomic: CGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|32829447|gb|CD969125.1|CD969125
EST:     CGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGTGGGCTTCATCGGCTCGCAC
genomic: CGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|211283078|gb|FL322113.1|FL322113
EST:     CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgt ... tttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttcgcgtgttccgaatcctgatttttggtgcccaattgctgtttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG
                      tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagcgtgatctcgactctggatctctatttcactcaccgttagacatgggcttgttcgcgtgttccgaatcctgatttttggtgcccaattgctgtttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC