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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcattatggtcttaaactattttttcttattttattgaagttcatgtatggagttaacatttccttacctgttcttatttggctgcaaaatgcag

Basic information

species Zea mays
transcript GRMZM2G053764_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T06 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G46940.1 (Glycine max), 5'ss of exon 3
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcattatggtcttaaactattttttcttattt-tattga--agttcatgtatggagttaacatttccttacctgttcttatttggctgcaaaatgcag------------------------
 ||| ||||| || || || ||  |||| ||||| |||||||||||||| || ||||| ||||| ||||||||||| |||||||| ||||| |||||||||| ||||  || ||  |||     |     || | | ||||||  |||| |  | || | |  | ||     ||  |||   |   ||  |   |  ||                           
-TGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGCTTTATCAACAAGATCTATCACCCAAATGTTGATGAGATGtaagcac-atagtagtaatgctctgaaaattgtctgtattgagtagtttacatgtgtattagatataagaataattgtgtgtcggtgcgtctgatctgatcatcttggataacattaatttcagg

upper sequence: GRMZM2G053764_T06 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G39370.1 (Glycine max), 5'ss of exon 2
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcattatggtcttaaactattttttcttattt-tattgaa-gttcatgtatggagttaacatttccttacctgttcttatttggctgcaaaatgcag
|||| ||||| || || || ||  |||| ||||| |||||||||||||| || ||||| || || ||||||||||| |||||||| ||||| |||||||||| ||||  || ||  |||     |     || | | ||||||    |   || |  | |      |    ||  || |   || |   |  | |||  | 
GTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCCGAATGTTGATGAGATgtaagcac-atagtagtaatgctctgaaaattgtctgtattgagtagttgcgtgtctattagctgatagaatatatgataagatatatttagataatatat

upper sequence: GRMZM2G053764_T06 (Zea mays), 5'ss of exon 2
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcattatggtcttaaactattttttcttattttattgaagttcatgtatggagttaacatt--tccttacctgtt---cttatttggctgcaaa-atgcag
|||| |||||| | || || ||||| |||||||| |||||||| ||||| || ||  | || ||||| | ||| || || ||||||||||||||||| |||||||    || |  | |    || ||||       |  | | |||| |      | |    | |  | ||||  ||||   | | ||||  ||     ||||||
GTGTGTGGAAGATAAGAGTTGAACTTCCTGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACCAAAATATACCACCCTAATGTCGATGAAATgtgagttcaatcgaatcagtagatcttttggaggagtgattatgttccttctccaaatcttgagtggtgcttatttgttatccctctttgtatgtggttatgcag

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|211363205|gb|FL271919.1|FL271919
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTANATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|32859414|gb|CD999095.1|CD999095
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|50325609|gb|CO520735.1|CO520735
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGAT                         GTCTGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
EST: gi|211174889|gb|FL306344.1|FL306344
EST:     CCGTCCATCGGCTTCATCAACAAGATTTATCACCCAAATGTCGATGAGAT                         GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT
genomic: CCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 239

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 687

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 863

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

GTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCCTAATGTCGATGAGATgtgagcatta ... caaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG