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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataacttcgtaccaatctgagaattttccactggttattagtaactagaaataacccatgtcataatcatgttgcttatttgtagctccagctctgcggtgttccataagtcatattttaatcgatgtgaatacgtgattaatggatctgccaatcttgcag

Basic information

species Zea mays
transcript GRMZM2G095969_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095969_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g06880.1 (Oryza sativa), 5'ss of exon 6
GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataacttcgtaccaatctgagaattttcca---ctggtt--attagtaactagaaataacccatgtca-taatcatgttgcttatttgtagctccagctctgcggtgttccataagtcatattttaatcg----atgtgaatacg-tgattaatggatctgccaatcttgcag
||||||||||||||| || |||||| ||||||||||||||||||| |||||| | |||| |||||||||||||||||| |||||||||| |  |   |   ||  | || | ||||      |||||   | || | |    |   |  | || ||  |||   |   |  || || |  |       || | |   | ||    ||  ||||  |||     |||| | |  | | | |  |  || |  |   |||||||
GCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTTCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAGgtaagctgtccgtgcgtcatgccgaaactttttgctgtctggtccaagtactcatctaatgcagtcaatttctctaaatttcacgagtaattttgcccttgatgctacagctctgcacgtctccaatttccatcagatcatgttattgagctcaatctttcatttctctgccttgcag

upper sequence: GRMZM2G095969_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 11
GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataacttcgtaccaatctgagaattttccactggttattagtaactagaaataacccatgtcataatcatgttgcttatttgtagctccagctctgcggtgttccataagtcatattttaatcg----atgtgaatacg-tgattaatggatctgccaatcttgcag
||||||||||||||| || |||||| ||||||||||| ||||||| |||||| | |||| |||||||||||||||||| |||||||||| |  |   |   ||  |   |   | |   ||   || |  |     | | | |    | ||  |||  |  |  | |||| |  |       || | |   | |||   ||  ||||| |||     |||| | |  | | | |  |  || |  | | |||||||
GCAAGTTCTTGAGGTTGTAGCTGGATGCAAAGGAATTGCTGACATTGAAGGCTTAAGTAAAACTCTGTACCACAACACGTGCAGgtaagctgtccgtgcgtcatgccttgctgtctggtctaagtactcatctaatgcagtcaatt-tctctaaattttactagtaattt-tgtccttgatgctacagctctgcatgtctccaattttcatcagatcatgttattgagctcaatctttcatttctctaccttgcag
















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|60340099|gb|DN207072.1|DN207072
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
EST: gi|78179334|gb|DV549707.1|DV549707
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCGTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
EST: gi|149089637|gb|EE178891.2|EE178891
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
EST: gi|76021691|gb|DT948861.1|DT948861
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
EST: gi|60341449|gb|DN208422.1|DN208422
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
EST: gi|78074889|gb|DV503323.1|DV503323
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG
EST: gi|211280306|gb|FL480836.1|FL480836
EST:     ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAG                         GCTCTTCTTTCCTCAAGATCTTGACGCGTCTGCTAATGCGCAGCTTGAGAG
genomic: ATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAG

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), 48 (downstream exon)
Score: 83

GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAGTGGTACTGCCGTCCAGGATTGCTGATGTCAGAGTGATTTTTTTATTATA


Block sizes: 47 (upstream exon), 37 (downstream exon)
Score: 97

GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAGTGGTACTGCCGTCCAGGATTGCTGATGTCAGAGTGATTTTTTTATTATA


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 57

GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAGTGGTACTGCCGTCCAGGATTGCTGATGTCAGAGTGATTTTTTTATTATA


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 37

GCAAGTTCTTGAGGTAGTGGCTGGAAGCAAAGGAATTTCTGACATAGAAGGCCTGAGTAGAACTCTGTACCACAACACATGCAGgtaagataac ... aatcttgcagGCTCTTCTTTCCTCAAGATCTTGACGCTTCTGCTAATGCGCAGCTTGAGAGTGGTACTGCCGTCCAGGATTGCTGATGTCAGAGTGATTTTTTTATTATA