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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatgatagtaacctccacgtaacagcaatacctcaactaattgagcagttacttatgtctgtttcgaatacgccag

Basic information

species Zea mays
transcript GRMZM5G846339_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846339_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 5'ss of exon 3
ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtat---taatgatagtaacctccacgtaacagcaatacctcaactaattg-------agcagttacttatgtctgtttcgaatacgccag
|||  |||| | |||||||||| |||||||||||||  |||||||||   || | ||||| |||||||| ||||||||||| || ||||||||||||||||||    |||  || ||    || ||  ||| |||  |  |||| | |  |       |  | ||| |||| |||||||  | || |||||
ATTAACAAATGAAAGCATGAGGATTGTTATGGTAACAATTATTGGAGTGCTCTTGGGCTTCTTCATTGGAATTTCATTCCCATCAGTCAGCATAACAAAGgtaagtataacaatggttttgtcaacagaactgcatcatgtcaattgaccgtaagagaataacttaattatctctgtttgaattatgccag
















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|76017486|gb|DT944656.1|DT944656
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|148945518|gb|EC890763.2|EC890763
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|149004827|gb|EE039332.2|EE039332
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|76915578|gb|DV166043.1|DV166043
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|149112888|gb|EE295684.2|EE295684
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211013669|gb|FL365579.1|FL365579
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211367815|gb|FL346930.1|FL346930
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211288821|gb|FL321201.1|FL321201
EST:     GCTTCCTTCSTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|211535602|gb|FL367699.1|FL367699
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|149070557|gb|EE158959.2|EE158959
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|148950258|gb|EC895810.2|EC895810
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
EST: gi|148965790|gb|EE016673.2|EE016673
EST:     GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC
genomic: GCTTCCTTCCTGTCTGCATAACAAAGCCGCCGCCATTATGATCTCCACATATGATGCTTAGCATTTGTCGCTCGCAGCTGTATTGCTCCTCTAGCTGCATCC

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: 48 (upstream exon), 49 (downstream exon)
Score: 72

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

ATTCCCAAACGGAAGCATGAGGCTTGTTATGGTAACGGTTATTGGAGCAGTCCTTGGCTTTTTCATTGGGATTTCATTCCCTTCGGTCAGCATAACAAAGgtattaatga ... aatacgccagCTTCACTTTCCAGATAGCTTTATTTCGTACATTGAAGACAAAGACGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACG