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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttcatttcttaactattttgtatcaaagctgtttttatcacgatgttatctgtgcggatctattttgtattttttatgcctaacaatgtttgta...

Basic information

species Zea mays
transcript GRMZM2G118286_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 5'ss of exon 8
TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttcattt--cttaactattttgta-tcaaagctgtttttatcacgatgttatctgtgcggatctattttgtattttttatgcctaacaatgtttgta-
 |||||||| ||||| || ||||||||||| |||||||| |||||||||||| ||||||| ||||| |||||||||||||||||||||||||| |||||||| || ||  |||  |||| | || || || |   || ||  ||  |     | |  |     |   | |   ||| | | || | |     | || | || | 
GTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttgtttttcttacccatattctaatttcagatgaattcgtt----tttggtagaaaccactgtgagttgaagtcttgaagatcgtccatatatgaaa

upper sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G03280.1 (Glycine max), 5'ss of exon 7
TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttcatttcttaactattttgtatcaaagctgtttttatcacgatgttatctgtgcggatctattttgtattttttatgcctaacaatgtttgta--
 |||||||| || || ||||||||||| |||||||| || ||   |||||| ||||||||||| ||||||||  | || || || || || | ||||||||| |  |  |  ||| | | ||||| | |  |  |   ||  || || |  || | | ||  |   |     |      | ||     |  ||| | ||   
ATATGGTCTTACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTCGGCCGTGTTGGACCACCTCTTCCATGCTCATTTATTAAGgt-aattatagatctgatcaattttatcttcatacaacttgaatgac-acattttttatgatggcttggggggagggagtaatatggtagcatggtagtttg

upper sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 5'ss of exon 8
TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttcatttcttaactattttgtatcaaagctgtttttatcacgatgttatctgtgcggatctattttgtattttt-tatgccta-acaatgtttgta
 ||||| || || || ||||||||||| || || || || |||| ||| |||||||| || || ||||||||||||||||| ||||| || | | | ||||| | ||   |  || |  | |    | | ||  || | ||    |     |  | |||  |      | |  | |  |  ||||| || |   |||||   
ATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTTCCTTGCTCCTTTGTAAAGgtaacctctttacctgatttgtccacttttaatactttgttagctatttattagtttgtatgtcgtagtctcttgtgatcatatgcttatatcttgtttcag

upper sequence: GRMZM2G118286_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 5'ss of exon 9
TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttcatttcttaactattttgtatcaaagctgtttttat-cacgatgttatctgtgcggatctattttgtattttttatgcctaacaatgtttgta----
 ||||| ||||| || | ||||||||| || |||||||| ||||||||||| |||||||| |||||||||||||||||||| ||||| || | ||||||||| || |  ||     || ||||||   |   |  || ||| || |  ||| ||     | |   |  | ||  ||  |   |  ||| ||  || | | |    
GTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTTCCTTGCTCATTTATTAAGgtaag-tggatg---aaaatattttac-ttgcatgtgctttaatgcgagatcttggacctacatgtgcacttcctagctgaaaaccctgaccttggtagaaaaca

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|211356217|gb|FL190937.1|FL190937
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCT
EST: gi|20802928|gb|BQ293978.1|BQ293978
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
EST: gi|211356219|gb|FL190939.1|FL190939
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGG
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGG
EST: gi|33091783|gb|CF051777.1|CF051777
EST:     GTTCGTATATTAAG                         TTGATCGACTGGCCTGAAGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: GTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
EST: gi|211130815|gb|FL468263.1|FL468263
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
EST: gi|211356216|gb|FL190936.1|FL190936
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
EST: gi|26456576|gb|CA828159.1|CA828159
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
EST: gi|78026723|gb|DV495110.1|DV495110
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
EST: gi|211356220|gb|FL190940.1|FL190940
EST:     ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAG                         TTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT
genomic: ACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCT

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: 116

TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCTCGGGGAGAAATTGTCATTGGAGGTCCAAATATAACTAAAGGCTATTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCTCGGGGAGAAATTGTCATTGGAGGTCCAAATATAACTAAAGGCTATTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCTCGGGGAGAAATTGTCATTGGAGGTCCAAATATAACTAAAGGCTATTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 88

TTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTACCTTGTTCGTATATTAAGgtcagcttca ... gtatttttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCTCGGGGAGAAATTGTCATTGGAGGTCCAAATATAACTAAAGGCTATTTCA