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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTATAACTAGTGCTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttcaatagaatcgtgcagctgacatctgtatacgtgctactagcaatgtagtcgagatgcaaatggaaattttgtttgtccaacaaagctgtta...

Basic information

species Zea mays
transcript GRMZM2G069758_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069758_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 9
GTGGTTATAACTAGTGCTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttcaatagaatcgtgcagctgacatctgtatacgtgctactagcaatgtagtcgagatgcaaatggaaattttgtttgtc--caacaaagctgtta--
||||| ||||||||||| |||||||||| |||||||||||| || ||||| ||||||||| || ||||||  ||  | |   |  ||      |||||| |  || ||||   ||   |||  |  |  || | | |||||  ||  | |||  ||   |  | |  |  
GTGGTAATAACTAGTGCACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAGgtaaactttta-acgtttatgtgatcaacatctttgcacatgctgtcag---tgtgctgcaattgaagacggaaaacttactggtctacagttattcagcaaaa
















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|33097992|gb|CF057952.1|CF057952
EST:     CCCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
EST: gi|86471052|gb|DY237422.1|DY237422
EST:     CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     CCCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     CTCTTATTGAAGGCAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACNNNNNNNCAGAG                         GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT
genomic: CTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttca ... ttttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTATAACTAGTGCTCTTATTGAAGGTAAGCTGCTCCTTATCGGAAGTCACAAAAAAACAGAGgtaactttcaatagaatcgtgcagctgacatctgtatacgtgctactagcaatgtagtcgagatgcaaatggaaattttgtttgtccaacaaagctgtta

- - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - GCTGCT