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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagatctgctatgcaggaataaatttgatgttttatattcactgtttttgtttcacaagcttgtctgttgcactctcactaagatttcttctttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAAGTCTGATAATCCTGGAAAAGGAATATGAAAATGCAATTAACACAAAAGG

Basic information

species Zea mays
transcript GRMZM2G033828_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033828_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 8
gttaagatctgctatgcaggaataaatttgatgttttatattcactgtttttgtttcacaagcttgt------ctgttgcactctcactaagatttcttctttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAAGTCTGATAATCCTGGAAAAGGAATATGAAAATGCAATTAACACAAAAGG
||    || || | | ||   | || | |    ||  ||| ||   |||| |||||||  | |||||      |  |  ||   ||  |     || || ||||||||||| |||||||||  ||||||| |||||||  ||| |||||||||||||  |||| || |||| ||||||||||||||||| |||||||||||||| || ||
gtatgaatgtgatcttcaaacacaattat----ttccatagtcgaggtttgtgtttcaggaacttgttgccatccatctcaacttccttgcttcttgttgtttgatgcagAGGGCTTGACATATTTTAAGAATTTGCTCGAGGAAGACTCATTGAAATTAAGTTTGCTAATGCTGGAAAAGGAATATGAGAATGCAATTAACACCAAGGG
















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|32930142|gb|CF034954.1|CF034954
EST:     CCCAGCTACTTCAGCATGCCAACAGGATAATTTGTCTTTCATCGATCCAG                         AAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAA
genomic: CCCAGCTACTTCAGCATGCCAACAGGATAATTTGTCTTTCATCGATCCAGgttaagatct ... tttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAA
EST: gi|71434758|gb|DR815808.1|DR815808
EST:     CCCAGCTACTTCAGCATGCCAACAGGATAATTTGTCTTTCATCGATCCAG                         AAGGCTTGACAGTTTTTAAGGATTTGCTTCAAGGAGACTCATTGAAACCAA
genomic: CCCAGCTACTTCAGCATGCCAACAGGATAATTTGTCTTTCATCGATCCAGgttaagatct ... tttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAA
EST: gi|32932368|gb|CF037180.1|CF037180
EST:     CCCAGCTACTTCAGCATGCCAACAGGATAATTTGTCTTTCATCGATCCAG                         AAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAA
genomic: CCCAGCTACTTCAGCATGCCAACAGGATAATTTGTCTTTCATCGATCCAGgttaagatct ... tttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttcacaagcttgtctgttgcactctcactaagatttcttctttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAAGTCTGATAATCCTGGAAAAGGAATATGAAAATGCAATTAACACAAAAGG
                                      tttcttcttt  CT-rich tract
                                 taagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagatctgctatgcaggaataaatttgatgttttatattcactgtttttgtttcacaagcttgtctgttgcactctcactaagatttcttctttgatgcagAAGGCTTGACAGTTTTTAAGGATTTGCTTCAGGGAGACTCATTGAAACCAAGTCTGATAATCCTGGAAAAGGAATATGAAAATGCAATTAACACAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA