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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgcttatgctgtgtaatctgcagttggcctttgtaactgtgatgtatggaacccggattgtttggctttggctttgtattttgtctaccag

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 3
ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgcttatgctgtgtaatctgcagttggcctttgtaactgtgatgtatggaacccggattgtttggctttggctttgtattttgtctaccag
 ||||||| || ||||||||||| || || |||||||| ||||| || ||||| || || || |||||||| ||||||||||||||||||  |||  || | ||||  ||  | ||||  || ||| | | |||| | |     ||| ||          |||| |||||  ||||||  |    
GTACTGCCTAATCCAGGTGACTCCGTATCGAGCCTCAGTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttatttttcctgta-aactttcagtatgcatttatcaatgtgttctt----accagg----------tttgactttgagttttgtgcag---
















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|37418983|gb|CF647165.1|CF647165
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052947|gb|FL232812.1|FL232812
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|71319015|gb|DR796255.1|DR796255
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211049994|gb|FL232801.1|FL232801
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAG-CAAGCCAAAGGCGTCCAT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCA-GCCAAAGGCGTCCAT
EST: gi|71435207|gb|DR816257.1|DR816257
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211049997|gb|FL232804.1|FL232804
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGS-GTNCCAT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGT-CCAT
EST: gi|211052943|gb|FL232808.1|FL232808
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|67019316|gb|CO448065.1|CO448065
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052951|gb|FL232816.1|FL232816
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTARCAGTCAGCCGAAAGS-GTCCCA
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCC-AAAGGCGTCC-A
EST: gi|31355022|gb|CD439379.1|CD439379
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211050000|gb|FL232807.1|FL232807
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|32915973|gb|CF020785.1|CF020785
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGTCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|71427496|gb|DR808546.1|DR808546
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211049999|gb|FL232806.1|FL232806
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052950|gb|FL232815.1|FL232815
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGSSGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052945|gb|FL232810.1|FL232810
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGS-GTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052956|gb|FL232821.1|FL232821
EST:     GCTTTAGTCCCAAGAGTAATCTACTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGA
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGA
EST: gi|78092605|gb|DV520979.1|DV520979
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052946|gb|FL232811.1|FL232811
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211049992|gb|FL232799.1|FL232799
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGS-GTNCCAT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGT-CCAT
EST: gi|71765073|gb|DR963010.1|DR963010
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211049998|gb|FL232805.1|FL232805
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|32868065|gb|CF007747.1|CF007747
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|62550552|gb|DN830972.1|DN830972
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|71310174|gb|DR791376.1|DR791376
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211049995|gb|FL232802.1|FL232802
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052953|gb|FL232818.1|FL232818
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052952|gb|FL232817.1|FL232817
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGSGTCCCAT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCC-AT
EST: gi|50339684|gb|CO534810.1|CO534810
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|33102995|gb|CF062955.1|CF062955
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|211052949|gb|FL232814.1|FL232814
EST:     GCTTTAGTCCCAAGAGTAATCTGMTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCA
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCA
EST: gi|32943595|gb|CF048414.1|CF048414
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
EST: gi|67024188|gb|CO452937.1|CO452937
EST:     GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAG                         GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT
genomic: GCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 71

ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

ATACTGCCGAACCCAGGTGACTCTGTCTCCAGCCTCAGCTTTAGTCCCAAGAGTAATCTGCTTGTGGCAACCTCCTGGGATAACCAGgtagctttgc ... tgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG