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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgccttcttcgctcaaactcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcag

Basic information

species Zea mays
transcript GRMZM2G039723_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039723_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g38600.2 (Oryza sativa), 5'ss of exon 3
AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgc-cttcttcgctcaaactcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcag
|||||||||||||||| ||| |||||||||||||||||||||||||||||||| |||||||||| ||  || ||||| ||| |||||||||| ||||||||| ||||| |     ||| ||    | | |    ||||    ||    | |   |   |||    |        | |     |||||
AATGCCGACCAGTACAGCCCCGACGAGCCCATCATCAGCAACGCCTCCTGCACCACCAACTGCCTCGCCCCCTTCGTGAAGATCCTCGACCAGAAGTTCGgtacgtgcgcacacgcgcgcatcagcgatcctcgaccaattttactctctctctctctctctgatgcttaaccaatcaatggcgcag

upper sequence: GRMZM2G039723_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0150g00500.t01 (Vitis vinifera), 5'ss of exon 4
AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgccttcttcgctcaa--actcaaactcaaaccatacgtaacggcgcatgcatactcatcc----gtcaccgtcaccgccaccgcag-------
||||| ||    ||||| |||| |||||||||||||||||| ||||| ||||| || || |||| ||  ||||| |||||| |||| ||||| || || |||   |       ||  |||   ||||||  | ||| | ||    ||     |   ||  |||||      | |   |||  |      ||        
AATGCTGAAACATACAATCCGGCCGAGCCCATCATCAGCAATGCCTCTTGCACCACTAATTGCCTCGCCCCATTTGTCAAGATCCTGGACCAGAAATTTGgtaattcatcaaatcattcatttactcaa-tttaaatcctataatacaatatacaaatcatcatcttcatatgaatatcaatggtgttccatatgatag

upper sequence: GRMZM2G039723_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0068g00680.t01 (Vitis vinifera), 5'ss of exon 4
AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtg------cgtgccttcttcgctcaaactcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcag
||||| ||| | ||||| |  || ||| ||||||||||||| || |||||||| ||||||||||  |  || |||||||||||||||||||| |||||||||       | | ||   ||||          | |     |    |   |  ||   || ||  |      | |     |    ||  ||||
AATGCAGACGAATACAATCATGATGAGTCCATCATCAGCAATGCTTCCTGCACAACCAACTGCCTTGCCCCCTTCGTCAAGGTCCTCGACCAGAAGTTCGgtaattttacatacccctttcgtctgtttgtcaccatggtcttccctccatcgctt-tgaatgatgggagcttaa----aaattcatggcag

upper sequence: GRMZM2G039723_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ13677 (Selaginella moellendorffii), 5'ss of exon 4
AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgccttcttcgctcaaactcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcag
|| ||||| || ||||  ||    ||||| |||||||||||||||||||||||||| |||||||  |  || |||||||| ||||| ||  | |||||||||  || |||      |  || |||   ||| | | || | ||    | | ||||   ||                          
AACGCCGAGCAATACAGTCCCACGGAGCCGATCATCAGCAACGCCTCCTGCACGACGAACTGCCTGGCTCCCTTCGTCAAAGTCCTGGATGAGAAGTTCGgtaagttcctc-----caaaagctctctctcgatcgatgc-tagaaactcttgcaacttccag-----------------------

upper sequence: GRMZM2G039723_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ29227 (Selaginella moellendorffii), 5'ss of exon 4
AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgccttcttcgctcaaactcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcag
|| ||||| || ||||  ||    ||||| ||||||||||| |||||||||||||| |||||||  |  || |||||||| ||||| ||  | |||||||||  || |||      |  || |||   ||| | | || | ||    | | ||||   ||                          
AACGCCGAGCAATACAGTCCCACGGAGCCGATCATCAGCAATGCCTCCTGCACGACGAACTGCCTGGCTCCCTTCGTCAAAGTCCTGGATGAGAAGTTCGgtaagttcctc-----caaaagctctctctcgatcgatgc-tagaaactcttgcaacttccag-----------------------

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 3 RNA-Seq libraries.


Block sizes: 34 (upstream exon), 33 (downstream exon)
Score: 8

AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgcct ... gccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGACCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 1046

AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgcct ... gccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGACCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 667

AATGCCGACCAGTACAACCCGGACGAGCCCATCATCAGCAACGCCTCCTGCACGACCAACTGCCGCGTGCCATTCGTCAAGGTCCTCGACCAAAAGTTCGgtgcgtgcct ... gccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGACCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC