Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcctgtcattcatcaccttgacaaatcttattgtccaaagtcgtttgtaattgatctgtgttgtaacatcatgcag

Basic information

species Zea mays
transcript GRMZM2G052750_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052750_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 5'ss of exon 18
TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcctgtcattcatcaccttgacaaatcttattg-tccaaagtcgtttgtaattgatctgtgttgtaacatcatgcag
||| ||||| ||||| |||   |||||||||||||||||||||||||||||||||||||| || ||||||||||| || || ||||| |||||||||||||| ||| |       ||||||| | | || | |||| ||| ||||||  |   ||| ||| || | | || |||| | ||||||
TGTCATGAATATTCTGGAGAACCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAGCTGGTTGCTTTTGTGAAAGGAACTCAGTTTGATCTTGTGgtaagattttcactgttcatcatcattaccagtcttgttgatccaaaaccacatgttattaatatat-ttataactttatgcag

upper sequence: GRMZM2G052750_T02 (Zea mays), 5'ss of exon 18
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 5'ss of exon 19
TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcctgtcattcatcacctt--gacaaatcttattgtccaaagtcgtttgtaattgatctgtgttgtaacatcatgcag
||| |  ||||| |||||    ||||||| |||||||||||| || || || ||||| ||||| ||||| ||||| || || ||||| |||||||| ||||| |||   |  |||||  |    ||  ||| | |  |||  ||    || | || ||| |  |        || | |  | |||
TGTCAAAAACATCCTAGAAAACCATGCTAACTATTTGATGTCAGGAAAAGAACTTTCCAAACTTGTTGCATTTGTTAAAGGCACTCAGTTTGATCTAGTGgtaagaaaacc-tcatttttggttttaggactattagtatcatcagtggttgcttctaacttgttcaccaccta-cttattacag
















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|87152673|gb|DY397462.1|DY397462
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
EST: gi|211446884|gb|FL341663.1|FL341663
EST:     TGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
genomic: TGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
EST: gi|211446492|gb|FK979151.1|FK979151
EST:     TGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
genomic: TGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
EST: gi|211253319|gb|FL352230.1|FL352230
EST:     TGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT
genomic: TGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCT

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: 123

TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

TGTTATGAACATTCTAGAGCGTCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... catcatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG