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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatctgtcaaatggaacactgtatactgctgtttttacatatatatttttgttacagttgtttcctcctgcag

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 13
GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatctgtcaaatggaacactgtatact---gctgtttttacatatatatttttgttacagttgtttcctcctgcag
||||| |||||||| || || ||||||||| ||||||| || |||||||| ||||||||||||| || |  |   || |  |  ||||| |        ||||||    ||| | |   | |||||||| |||  ||||  ||
GATCCACAAGTTGTCACGGGCTCACATGATTCAACTATCAAGTTCTGGGACCTTGTAGCTGgta-tttactttagaattttactactgtgtttcttgagtgttttcttgtatctgtccct-ttacagttatttt-tcctatag
















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|78021762|gb|DV490149.1|DV490149
EST:     TTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|116814103|gb|EC856623.1|EC856623
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|71432304|gb|DR813354.1|DR813354
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|60357310|gb|DN224283.1|DN224283
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|93012802|gb|EB638322.1|EB638322
EST:     GATACAATTATTAAATTTTGGGATCTGGTAGCTG                         GGAGGAGTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: GATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|71757914|gb|DR955851.1|DR955851
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|32933221|gb|CF038033.1|CF038033
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTA
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTA
EST: gi|211016045|gb|FL237689.1|FL237689
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|148950912|gb|EC896542.2|EC896542
EST:     ATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: ATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|148943610|gb|EC888673.2|EC888673
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
EST: gi|71432303|gb|DR813353.1|DR813353
EST:     TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG                         GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG
genomic: TGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGG

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: 157

GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 69

GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTGgtaattcatc ... cctcctgcagGGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA