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'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTGGAAAACAACAATATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcataacctgaatattggaaggatgcacaaaattttgtattttttttctaacatagaccttttgcatctttggacag

Basic information

species Zea mays
transcript GRMZM5G809695_T03
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809695_T03 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 21
AAAACTGGAAAACAACAATATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttca-taacctgaatattg--gaaggatgcacaaaattttgtattttttttctaacatagaccttttgcatctttggacag
||| ||  |||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||| || | ||||| ||| |||   |||| ||   |   | | | | ||||||  || ||||   |  | ||  | | ||  |||
AAATCTCAAAAACAACAACATAACTGGGGATGTCTCTTCACTGATGAACTGCTTCAGCCTCAATATCTTgtaagttgaataaccagaaaatttttgaagcatatgctccagtatatgttttttg-ctcacattatctatctgt-tttatgatcag
















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|71769229|gb|DR967166.1|DR967166
EST:     ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTT                         AAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
genomic: ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
EST: gi|211021287|gb|FL334113.1|FL334113
EST:     ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTT                         AAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
genomic: ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
EST: gi|211538240|gb|FL353975.1|FL353975
EST:     ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTT                         AAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
genomic: ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
EST: gi|28873715|gb|CB329664.1|CB329664
EST:     ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTT                         AAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
genomic: ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
EST: gi|31405872|gb|CD484604.1|CD484604
EST:     ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTT                         AAATGTGTCATACAATAAT
genomic: ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAAT
EST: gi|32164946|gb|CD670264.1|CD670264
EST:     ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTT                         AAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT
genomic: ATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTT

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: 49 (upstream exon), 49 (downstream exon)
Score: 2441

AAAACTGGAAAACAACAATATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTTCACACGGTTTTCACATGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

AAAACTGGAAAACAACAATATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTTCACACGGTTTTCACATGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

AAAACTGGAAAACAACAATATAACTGGCGATGTCTCTTCTCTGATGAACTGCTTCAGCCTCAATATCTTgtaatttcat ... ctttggacagAAATGTGTCATACAATAATTTGGCTGGTGCTGTCCCTACTGACAACAACTTCACACGGTTTTCACATGACAG