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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCGCTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttgtcagtactaaagctcaagtcaaccatgaagggtcgattctgatgcaccatataataaacttgttttacag

Basic information

species Zea mays
transcript GRMZM2G304362_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 9
GTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCGCTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttgtcagtactaaagctcaagtcaaccatgaagggtcgattctgatgcaccatataataaacttgttttacag
 |||||| | |||||||| ||||||||||  |||||||||||||| || ||||||||||| || ||||||||||||||||| ||||||||  ||||||||||||||||||| ||| ||   ||| |  |||||| | || | |  ||  | |     |  || ||||  || | || |||
TTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTGCTGTCTGCAATCTGGCATCTATTGCTTTACCACGTTTTGTAAGGGAAAAGgtatatcttgttagtgctttggctgatttcaaccctaaatgttgtatgtttacatgtctgatcataagattctgttgcag
















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|32933128|gb|CF037940.1|CF037940
EST:     CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAG                         GATGTTCCATTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
genomic: CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
EST: gi|211102666|gb|FK948700.1|FK948700
EST:     CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAG                         GATGTTCCATTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
genomic: CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
EST: gi|33098100|gb|CF058060.1|CF058060
EST:     CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAG                         GATGTTCCATTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
genomic: CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
EST: gi|32931387|gb|CF036199.1|CF036199
EST:     CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAG                         GATGTTCCATTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
genomic: CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
EST: gi|211102667|gb|FK948701.1|FK948701
EST:     CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAG                         GATGTTCCATTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
genomic: CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
EST: gi|32930756|gb|CF035568.1|CF035568
EST:     CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAG                         GATGTTCCATTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA
genomic: CTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCA

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: 365

GTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCGCTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCAAAAAATAGATATTTTGATTTTGAGAAGCTAGCTGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 112

GTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCGCTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCAAAAAATAGATATTTTGATTTTGAGAAGCTAGCTGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 87

GTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCGCTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCAAAAAATAGATATTTTGATTTTGAGAAGCTAGCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

GTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCGCTGTCTGCAACCTAGCATCTATTGCTTTACCTCGTTTTGTTCGGGAAAAGgtatatcttg ... tgttttacagGATGTTCCGTTGGAGTCCCATCCATCTAAGCTTGTGGGTAGCAGTGATTCAAAAAATAGATATTTTGATTTTGAGAAGCTAGCTGAG