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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacctgacccaacacaatttttttaattgaaaaattgatggtatttccacaacttacattcctcttatttgacatgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATCTTACATGCTAGCTGAA

Basic information

species Zea mays
transcript GRMZM2G037342_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 6
gtttgtacctgacccaacacaatttttttaat---tgaaaaattgat-----ggtatttc--cacaacttac-attcctcttatttgacatgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATCTTACATGCTAGCTGAA
||||||||   || | |||  || |  || ||   || |  ||  ||     |  ||||    | || |  | | |||    |||  || | ||  |||||||||| || |||||||||||||| ||||||||||| |||||||| || ||||||||||| ||||||
gtttgtacaacacaccacattatgtggttgatatttgtatgatcaatcaccagacattttataataattctctaatccatgaattataccttcaatccagGCATTCCACTGATCGTGAAGTTTCTATTATGATGCTCATGGCTTACTTGTCTTACATGCTTGCTGAA
















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|71301742|gb|DR786939.1|DR786939
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|78119306|gb|DV537690.1|DV537690
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCACCCGATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATC
EST: gi|32866161|gb|CF005843.1|CF005843
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|20300970|gb|BQ163913.1|BQ163913
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|71426858|gb|DR807908.1|DR807908
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|18964389|gb|BM660977.1|BM660977
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|149058822|gb|EE156843.2|EE156843
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|76912611|gb|DV164818.1|DV164818
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATC
EST: gi|149015463|gb|EE045330.2|EE045330
EST:     TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG                         GCATTCACCCGATCGTGAAAGTT-CCATTATGATGCTAATGGCTTATTTAT
genomic: TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAGgtttgtacct ... tgcaccccagGCATTCAACCGATCGTGAA-GTTTCCATTATGATGCTAATGGCTTATTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattgatggtatttccacaacttacattcctcttatttgacatgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATCTTACATGCTAGCTGAA
                                 tcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacctgacccaacacaatttttttaattgaaaaattgatggtatttccacaacttacattcctcttatttgacatgcaccccagGCATTCAACCGATCGTGAAGTTTCCATTATGATGCTAATGGCTTATTTATCTTACATGCTAGCTGAA

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