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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagagaagggttgtcatttatatgcacttttactttgtctgatacagtgatatctcgtgtcctgatttgcacaactctgctgattatatggtactgtacctttgctagttttaagatattgttggagcttgggtagggcctatttgttagtgtctatcatctttctctttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGCGCCCACCGGTCAAGAT

Basic information

species Zea mays
transcript GRMZM2G064371_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064371_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 2
gtaaaagagaagggttgtcatttatatgcacttttactttgtctgatacagtgatatctcgtgtcctgatttgcacaactctgctgattatatggtactgtacctttgctagttttaagatattgttggagcttgggtagggcctatttgttagtgtctatcatctttctctttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGCGCCCACCGGTCAAGAT
                                                                                  |   |  || | | | | ||  || |   | | |   || |   | ||        || |  || ||   | | | | ||   |||    || | |||||| ||||||||| ||||||| || |||||||| ||| ||||| ||||||||||||| ||  ||||  |
----------------------------------------------------------------------------------gtaaaacatgttggattttattttggtgggatgtgcaatttacatcga--------agtgtttaattac-attatgtttcgatttt----ttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT
















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|211516136|gb|FL164980.1|FL164980
EST:     CCGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCA
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211236272|gb|FL396917.1|FL396917
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211440980|gb|FL373018.1|FL373018
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTNAATGATCCACATCAG                         GTCTGGAATTGCTA-TGAGCACGAAGATTTGCAAGTTCTTGTGATCATATC
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATT-CTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATC
EST: gi|211063592|gb|FL411757.1|FL411757
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|78180987|gb|DV551360.1|DV551360
EST:     CCGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCA
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|8577300|gb|BE129937.1|BE129937
EST:     CCGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCA
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|12047263|gb|BF729402.1|BF729402
EST:     CCGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGGGATCATATCA
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|6918664|gb|AW400194.1|AW400194
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|9952569|gb|BE639257.1|BE639257
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAA
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAA
EST: gi|211490328|gb|FL379763.1|FL379763
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211106738|gb|FL429079.1|FL429079
EST:     CCGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGC
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGC
EST: gi|32848146|gb|CD987827.1|CD987827
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211288157|gb|FL392359.1|FL392359
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211032073|gb|FL384599.1|FL384599
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211430009|gb|FL445195.1|FL445195
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211236771|gb|FL420040.1|FL420040
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211507889|gb|FL229580.1|FL229580
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211438792|gb|FL370296.1|FL370296
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAG
EST: gi|211516143|gb|FL164987.1|FL164987
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|87152705|gb|DY397494.1|DY397494
EST:     CCGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCA
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|74034934|gb|DT535424.1|DT535424
EST:     GTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCA
genomic: GTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211439420|gb|FL403340.1|FL403340
EST:     CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAG                         GTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCCTATCG
genomic: CTGTCTTTCAGAATACCACATTTTCGATCCCTGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211516146|gb|FL164990.1|FL164990
EST:     CGTCTTTCAGAATACCACATTTTCGATCCCCTGTAAATGATC-ACATCAG                         GTCTGGAATTCT
genomic: TGTCTTTCAGAATACCACATTTTCGATCCC-TGTAAATGATCCACATCAGgtaaaagaga ... tttcttgcagGTCTGGAATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagcttgggtagggcctatttgttagtgtctatcatctttctctttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGCGCCCACCGGTCAAGAT
                            tgtctatcatctttct  CT-rich tract
                  tatttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagagaagggttgtcatttatatgcacttttactttgtctgatacagtgatatctcgtgtcctgatttgcacaactctgctgattatatggtactgtacctttgctagttttaagatattgttggagcttgggtagggcctatttgttagtgtctatcatctttctctttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGCGCCCACCGGTCAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA