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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATAATGGAAGCTGTTAATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgcttctcgctgttattgtcgtgctgcgccagttcttagtttaattgctatataaggtagcaggtataagatattagcgcctcgtttcatgcagtaaagtgaaacagcgtagtgtttcaatctagtgctctatattttgttcag

Basic information

species Zea mays
transcript GRMZM2G051276_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051276_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g07350.1 (Oryza sativa), 5'ss of exon 2
GTTATAATGGAAGCTGTTAATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgcttctcgctgttattgtcgtg-ctgcgccagttcttagtttaattgctatataaggtagcaggtataagatattagcgcctcgtttcatgcagtaaagtgaaacagcgtagtgtttcaatctagtgctctatattttgttcag
||||||||||||||||||||||||||||||||||| ||||| || || |||||||||||||| |||||||||| ||||||||  ||  | |||| ||  |  |  | | |  ||  ||  ||| ||| ||   |    | | |   | |  |        | |||| |                                                    
GTTATAATGGAAGCTGTTAATAAGCCACGCAATATTCACTACAAGGGAGTTGCAGACCTGGTCACAGAgtaaggatgcttcttacttgtgttgttgtttccccatctgatgctaacttggttgttatttatcattcttgatctttcaaaagaaaaaagt-tatcatcct---------------------------------------------------
















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|22491531|gb|BU051454.1|BU051454
EST:     AAGGTGTTGCAGACCTGGTGACAGA                         CACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTC-CCAAGAACTT
genomic: AAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT
EST: gi|211169546|gb|FL047612.1|FL047612
EST:     AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGA                         CACAGACAAGTTGAGTGAATCAGTCATTTTGGAAG
genomic: AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAG
EST: gi|19350800|gb|BM895332.1|BM895332
EST:     AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGA                         CACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT
genomic: AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT
EST: gi|211169549|gb|FL047615.1|FL047615
EST:     AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGA                         CACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAAACT
genomic: AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAA-CT
EST: gi|89106256|gb|DY576473.1|DY576473
EST:     AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGA                         CACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT
genomic: AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT
EST: gi|101394982|gb|EB819425.1|EB819425
EST:     AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGA                         CACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT
genomic: AATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTT

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), 48 (downstream exon)
Score: 36

GTTATAATGGAAGCTGTTAATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTTCAAAGACCACCTCATACTTGGGGAGGAAGGCGGCCTTGTTGGAGATTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

GTTATAATGGAAGCTGTTAATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTTCAAAGACCACCTCATACTTGGGGAGGAAGGCGGCCTTGTTGGAGATTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

GTTATAATGGAAGCTGTTAATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTTCAAAGACCACCTCATACTTGGGGAGGAAGGCGGCCTTGTTGGAGATTCC


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

GTTATAATGGAAGCTGTTAATAAGCCACGCAATATCCACTATAAAGGTGTTGCAGACCTGGTGACAGAgtaagaatgc ... ttttgttcagCACAGACAAGTTGAGTGAATCAGTCATTTTGGAAGTTGTCACCAAGAACTTCAAAGACCACCTCATACTTGGGGAGGAAGGCGGCCTTGTTGGAGATTCC