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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgatatcctagatgaattctaacatcaagaactaaatatcatgaatctaaattatatatttcttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAAAATATGGGCTATCAATTTACTCGTGGGATGAATTTCTGTCCCTG

Basic information

species Zea mays
transcript GRMZM5G861300_T01
intron # 7
splice site 3'
intron type U2

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|149085681|gb|EE175195.2|EE175195
EST:     CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAA                         CGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAA
genomic: CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAA
EST: gi|148986409|gb|EE030148.2|EE030148
EST:     CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAA                         CGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAA
genomic: CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAA
EST: gi|8401341|gb|BE056975.1|BE056975
EST:     CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAA                         CGATCGTAAGTTTCTGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAA
genomic: CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 177

CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAAAATATGGGCTATCAATTTACTCGTGGGATGAATTTCTGTCCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAAAATATGGGCTATCAATTTACTCGTGGGATGAATTTCTGTCCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAAAATATGGGCTATCAATTTACTCGTGGGATGAATTTCTGTCCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

CTCGTGAAGACTTTACCTAAGTCAAATGAGTTCTTAAAAAgtaagtttga ... cttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAAAATATGGGCTATCAATTTACTCGTGGGATGAATTTCTGTCCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaacatcaagaactaaatatcatgaatctaaattatatatttcttattgtagCGATCATAAGTTTCGGCAAGGTAACTCAAGAACAGAAGGGAGAAGTCCAAAAATATGGGCTATCAATTTACTCGTGGGATGAATTTCTGTCCCTG
                                          tttcttatt  CT-rich tract
             aactaaatatcatgaa  TA-rich tract