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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatgggaaaacaactcagtagtaatgcttttcgaattataaattatttctatttcacacgatgcttctag

Basic information

species Zea mays
transcript GRMZM2G020002_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g59340.1 (Oryza sativa), 5'ss of exon 10
GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatgggaaaacaactcagtagtaatgcttttcgaattataaattatttctatttcacacgatgcttctag
||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||||| ||| ||||||||||||||   |  |||| |     |   || || |  |||| |   || ||| ||| ||| |  |   ||||||
GGCAGAGAGTCATTGGTGAACCTGTGGTTTCTGGGCTAGTACTTGATGATTCTTGGCTTTGGGATCCGGACTTCATGATAGCTTCAAAgtaaataaaagcacaaatttaatgctttgtttatgcaattgtggtttcttt-tatctcatatcacatttctag

upper sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 7
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 5'ss of exon 7
GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatgggaaaacaactcagt--agtaatgcttttcgaattat------aaattatttctatttcacacgatgcttctag
| ||||  || || || || ||||| || |||||| || | |||||||||  |||||||||||||||||||||||| ||||| || ||||||         ||  || ||  |  ||    || | | ||||      | ||| |     |||  | | ||  |||   
GACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAAgtaataaatccttcagttctgttaatcaaatgattcccatttattctttcagattttcaaagtttttctcaatatttcag-

upper sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 5'ss of exon 7
GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaa-atgggaaaacaactcagtagtaatgcttttcgaattataaatta---tttctatttcacacgatgcttctag----------------
| ||||| || || || || || || ||||||||  |||| |||||||||||| |||| ||||||||||||||||  |  ||  ||||| || ||   | |     ||  |  |  |  | |    | | |  || |   ||| ||         |   || |                  
GACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAAgcaagatctcatactccttccattttcttcttctcttcactttctatcacattttttaacctttgtcaacattatgatcttttcatgtttcag

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|18659090|gb|BM500149.1|BM500149
EST:     GTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA                         GTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCA
genomic: GTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatggga ... atgcttctagGTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCA
EST: gi|31355355|gb|CD439712.1|CD439712
EST:     GTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACAATTGCTTCAAA                         GTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCA
genomic: GTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatggga ... atgcttctagGTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCA

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: 39 (upstream exon), 35 (downstream exon)
Score: 25

GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatggga ... atgcttctagGTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCAAGCTGCTCTTTCATCGGGAATTCTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 210

GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatggga ... atgcttctagGTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCAAGCTGCTCTTTCATCGGGAATTCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatggga ... atgcttctagGTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCAAGCTGCTCTTTCATCGGGAATTCTACAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 43

GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAAgtaaatggga ... atgcttctagGTACGTGATGAGTCCTCCAATCCGGGAAGCAGGGCATGGTAAAGCACTCCAAGCTGCTCTTTCATCGGGAATTCTACAG