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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttgcagtttatgttagcagaatgaacatttaacttcactgtttaaacattctactaaatttttctggctgtttcaccgtgcag

Basic information

species Zea mays
transcript GRMZM2G117507_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 11
AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttgcagtttatg-ttagcagaatgaacatttaacttcactgtttaaacattctactaaatttttctggctgtttcaccgtgcag
||||||||||||||||   ||||||||| | || | |||||||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| || ||||| |||||| | | || ||     ||||| |||| |  || | ||| || ||    |   | || |||||||      | || |||||
AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagac----tgtaacatatttctggtccacactccctgcag

upper sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 11
AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttgcagtttatgttagcagaat-gaacatttaacttcactg--tttaaacattctacta--aatttttctggctgtt--tcaccgtgcag
 |||||||||||||||   ||||||||| | |||| |||||||||||| ||||||||||| |||||||| |||||||||||||| || |||||||| || ||||| | | | || |||| |     | | ||||||| |  ||   ||  ||  |  ||  || ||  ||  | ||||| ||||  || |  |||||
GATTGATCTACTTGGTCAAGTAGATGAGCTATTCTTTGATATCTATGATAGATATGAACCCGTGAATGAGCCATCTCTTGATAACTGTTTTGTCTCAACTgtaagttctacggtgtatgattttgcacttgaacattaagtttggttgtgttggagtataatagtataaacatctctggttgttattctctctgcag
















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|78022940|gb|DV491327.1|DV491327
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|60351459|gb|DN218432.1|DN218432
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|5668482|gb|AI931997.1|AI931997
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32930550|gb|CF035362.1|CF035362
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|6827485|gb|AW331128.1|AW331128
EST:     GATATGAACCAGNGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32842698|gb|CD982379.1|CD982379
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32940482|gb|CF045301.1|CF045301
EST:     ATATGAACCAGTGAATGAACCAGTCTGTTGGTAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: ATATGAACCAGTGAATGAACCA-TCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|95108161|gb|EB740390.1|EB740390
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|5296179|gb|AI782859.1|AI782859
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|211070323|gb|FL464130.1|FL464130
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32932215|gb|CF037027.1|CF037027
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|31352817|gb|CD437174.1|CD437174
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|5915586|gb|AW053227.1|AW053227
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|108953371|gb|EC364705.1|EC364705
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|60346246|gb|DN213219.1|DN213219
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|211417699|gb|FL464427.1|FL464427
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|29946000|gb|CB815928.1|CB815928
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|60353508|gb|DN220481.1|DN220481
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|6865134|gb|AW360484.1|AW360484
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|5791273|gb|AI978065.1|AI978065
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|5871056|gb|AW017497.1|AW017497
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|13515652|gb|BG517928.1|BG517928
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32940403|gb|CF045222.1|CF045222
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|6056470|gb|AW090860.1|AW090860
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|6194638|gb|AW146742.1|AW146742
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|5901301|gb|AW042401.1|AW042401
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32934162|gb|CF038974.1|CF038974
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|32934507|gb|CF039319.1|CF039319
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
EST: gi|211280268|gb|FL478208.1|FL478208
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACA                         AGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAAC

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: 507

AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAACATGTATACAATGATCACCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 757

AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAACATGTATACAATGATCACCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 504

AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAACATGTATACAATGATCACCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttg ... caccgtgcagAGCTATGATGCCACCACACATTTTGAGACAACTGTAACAGATGTTCTGAACATGTATACAATGATCACCGGAAAG