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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatacctctatttcttacctatttcatacttctattttaggattatgtaataaattttaatccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG

Basic information

species Zea mays
transcript GRMZM2G099481_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099481_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g38710.2 (Oryza sativa), 3'ss of exon 3
gtttatacctctatttcttacctatttcatacttctattttaggattatgtaa--taaattttaatccattatt-----agGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG--------------------------
|| | | || ||||||||||   ||   ||   | |||||| |   | |||||  | | ||||  | | || ||     ||||||| |||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| |||||                          
gtctgtgcccctatttcttaataataatat---tttattttggagatctgtaaattgatttttctttctttttttactaagGTTGAGGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTCATTTCTGATGTGGATGGAACCATTACAAGGTAAAGTTCAACTTAGTATGTTTAGA

upper sequence: GRMZM2G099481_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 3
gtttatacctctatttcttacctatttcatacttctattttaggattatgtaa--taaattttaatccattatt-----agGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG
|| | | || ||||||||||   ||   ||   | |||||| |   | |||||  | | ||||  | | || ||     ||||||| |||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| |||||
gtctgtgcccctatttcttaataataatat---tttattttggagatctgtaaattgatttttctttctttttttactaagGTTGAGGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTCATTTCTGATGTGGATGGAACCATTACAAG

upper sequence: GRMZM2G099481_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g02800.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------gtttatacctctatttctta----cctatttcatacttctattttaggattatgtaataaattttaatccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG
                           |||  |  || || | | |     || ||  || | | | | ||   | |   |||  || |||   |  ||   |||||||||| ||||||||||| ||||| |||||||| | |||||| || || ||||| || || || ||||| | 
gtctgatattggtgtctaatattcaaatttcaatttcaatatgtaaaaagtctgttggatgcctttctgtttcaactgc-taaggaactttcg-cttttgacagGTTGATGCTCATATTTACTTATGGAAGTGGAATGCAAGAATTGTAATTTCAGATGTTGACGGGACAATAACCAA

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: 104

TTTGATTCCCACAAGTGAACAGGTAGCATCTTTAAATCTGAAGGAGGGCCAAAACTTGGTGACCTTTAGCTTCTCCACCAGAGTTCTTGGGAAGCAACAGgtttatacct ... ccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

TTTGATTCCCACAAGTGAACAGGTAGCATCTTTAAATCTGAAGGAGGGCCAAAACTTGGTGACCTTTAGCTTCTCCACCAGAGTTCTTGGGAAGCAACAGgtttatacct ... ccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

TTTGATTCCCACAAGTGAACAGGTAGCATCTTTAAATCTGAAGGAGGGCCAAAACTTGGTGACCTTTAGCTTCTCCACCAGAGTTCTTGGGAAGCAACAGgtttatacct ... ccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

TTTGATTCCCACAAGTGAACAGGTAGCATCTTTAAATCTGAAGGAGGGCCAAAACTTGGTGACCTTTAGCTTCTCCACCAGAGTTCTTGGGAAGCAACAGgtttatacct ... ccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctatttcatacttctattttaggattatgtaataaattttaatccattattagGTTGATGCACATATTTACTTGTGGAAATGGAATGCTAAAATTGTGATATCTGATGTGGATGGCACCATAACAAG
                tattttaggattatgt  TA-rich tract