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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgttctgtggatcagtgctttctctgtcttaataccattgggcatatttaagttgtttttcttgttttacag

Basic information

species Zea mays
transcript GRMZM2G065130_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065130_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 5'ss of exon 37
CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgta--catgcgttctgtggatcagtgctttctctgtcttaataccattgggcatatttaagttgtttttcttgttttacag--------------------
 ||  |||||||||| ||||||||||||||||||||||||||||||  ||||  |||||   |||||||| ||  ||| ||  |||  |||||| | ||||||  |||  ||| | |  |  | |  |||||   |  |  || | || |  | |  |   |  ||||   ||   |||                      
TGACATGATTCCTTCCAGTTGCATTCAAATGCGCAATGTCATTCTTGATGCTCATCCACAAGACATGAGAGTGGTAGATCCAGCTAGTCCTAATTTGAAGgtagccatttgtttt-tacaataatattttcttcattctcctaactttagttagagatttttgtttttgactgaaatacttttagggctttgcctgacagt

upper sequence: GRMZM2G065130_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S85_31V6.1 (Physcomitrella patens), 5'ss of exon 46
CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgta---catgcgttctgtggatcagtgctttctc----tgtcttaataccattgggcatatttaagttgttttt-cttgttttacag------------------------------------------------------------
 |||||||||||  ||   || ||||| ||||||||| | |||||||| ||||||||||| |||||| |||| || || |||| ||| |||||| | ||||||    || | |  | |  | |       | |     |  | ||  |   |||  ||| |||||   ||   |  ||  |||   |                                                            
TGATGTGATTCCCCCATCCTGTATTCAGATGCGCAATCTAATTCTTAGCGCTTTTCCACGCAACATGCGACTTCCTGATCCTTTTACACCTAATTTGAAGgtagcatattcatattttcaaccttcaaactttgcagatagcctatcaattttgttcatttttaaaaagtaaatatttcctttgtggctgttatatgtaaattggaaggcacaaaagtcagctatctaaggcgtggtgtttaatcag
















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|211183840|gb|FL001297.1|FL001297
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
EST: gi|211183842|gb|FL001299.1|FL001299
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
EST: gi|166702237|gb|EG275237.1|EG275237
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
EST: gi|15499314|gb|BI595827.1|BI595827
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
EST: gi|211183841|gb|FL001298.1|FL001298
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTT

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), 48 (downstream exon)
Score: 200

CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTTGATGGTGCCCTTAAATCAAAGCAGTTGAAGACTGAGGTTGATGAATATC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 98

CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTTGATGGTGCCCTTAAATCAAAGCAGTTGAAGACTGAGGTTGATGAATATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTTGATGGTGCCCTTAAATCAAAGCAGTTGAAGACTGAGGTTGATGAATATC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 94

CGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACCCCTAATCTAAAGgtacatgcgt ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCGGATGTTGATGGTGCCCTTAAATCAAAGCAGTTGAAGACTGAGGTTGATGAATATC