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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataacaattgtatctcaggatgcaggggtgaacttctttgttagaattgtgtgggcgccctttgttaggttgtttatgtttactcgattttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCACAAAAAG

Basic information

species Zea mays
transcript GRMZM2G011173_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011173_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g05650.1 (Oryza sativa), 3'ss of exon 4
---aataacaattgtatctcaggatgcaggggtgaacttctttgttagaattgtgtgggcgccctttgttaggttgtttatgtttactcgattttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCACAAAAAG
     | || |||  || |  | |||    |||  | || ||||| | |||| | ||     |  || | | || || |   |  ||||  |||  |  |||| |||||||||||||| |||||||| ||||||||||| |||||||||||||| |||||
tcttttcactattacatgttggaatgtcctggttcaattatttgtgaaaattttatgaaaatcacttctcaagtcgtgt---tccactccctttcctcggcagAATACTGAACGCATATGCCAAAGTGCCTCCAAAACCAAAAGTGCCTTCCACGAAAAG
















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|91050350|gb|EB160768.1|EB160768
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|89248124|gb|DY619910.1|DY619910
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|71419808|gb|DR804903.1|DR804903
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|71435432|gb|DR816482.1|DR816482
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|71320866|gb|DR797150.1|DR797150
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|76013659|gb|DT940829.1|DT940829
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|71313019|gb|DR793034.1|DR793034
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|211502577|gb|FL311927.1|FL311927
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: -GGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|211145073|gb|FL314893.1|FL314893
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|67034610|gb|CO463160.1|CO463160
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|78091120|gb|DV519494.1|DV519494
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|74241849|gb|DT649763.1|DT649763
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|93016793|gb|EB642313.1|EB642313
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|71768256|gb|DR966193.1|DR966193
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|94477701|gb|EB706659.1|EB706659
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|101382184|gb|EB813148.1|EB813148
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
EST: gi|87153649|gb|DY398438.1|DY398438
EST:     TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTCTTTGGAAG                         GATACTGAACGCTTACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC
genomic: TGGTTTTACAATCAACATGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggctt ... ttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtgtgggcgccctttgttaggttgtttatgtttactcgattttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCACAAAAAG
                                           ttttattt  CT-rich tract
                                          attttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataacaattgtatctcaggatgcaggggtgaacttctttgttagaattgtgtgggcgccctttgttaggttgtttatgtttactcgattttatttgcagGATACTGAACGCATACGCCAAAGTACCTCCAAAACCGAAAGTGCCTTCCACAAAAAG

aataaca
- - - - - - - - - ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttt