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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatcatatatgaaatccgtcatggcttcttctaaagttcttccaacaattctctccacttgtaggttatggtctgtgttggagtaccatgtaagc...

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 3
ATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatcatatatgaaatccgtcatggcttcttctaaagttcttccaacaattc-tctccacttgtaggttatggtctgt-gttggagtaccatgtaagc
 ||||||||||| | |||||||||||||||||||||| ||||||||||   |||||| ||||||| |||||||| |||||||| |||||| ||   || ||||||| | || | ||||||   |  |   ||| |  | |     |||     ||  |  |  | |  ||    || |  ||   | ||  |  ||||    
GTTTTGTTAGTGCAAAGGGGAAACTGTAAGTTCACTAAAAAAGCTAAGAATGCTGAAGCTGCTGGGGCTTCTGCTATTATAATCATCAATCATGTCCATGgtatgccttatttgtgaaattatttgtaaattcatacatataatgtcctttgctttatacctgcgttcagcagctgattagttagtagatcaagatgttg--
















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|149049844|gb|EE048531.2|EE048531
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|89758526|gb|DY687677.1|DY687677
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|76282122|gb|DV021690.1|DV021690
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|211335511|gb|FL455439.1|FL455439
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|211297692|gb|FL447045.1|FL447045
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|148956514|gb|EC902353.2|EC902353
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|149081128|gb|EE170234.2|EE170234
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
EST: gi|71422117|gb|DR805619.1|DR805619
EST:     GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACG                         AGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA
genomic: GGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCA

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: 192

ATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 299

ATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

ATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 263

ATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCAATGATAAGCACGgtatgcatca ... ccacctgcagAGTTATACAAGATGGTATGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTC