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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgtaaaaaaaaaagagtgaagggttatgattagacagaaagtgcatcacctcactgcaaaaatatgtgaatggattactttgatttgtggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATGCAG

Basic information

species Oryza sativa
transcript LOC_Os05g43560.1
intron # 16
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|87027882|gb|CI276238.1|CI276238
EST:     TTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: TTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|88261850|gb|CI365426.1|CI365426
EST:     GATTT-TGAT-GAG                         GTTGAG-AAATGATAGATACCACATACACTGCAAATATTAAATCAATGATG
genomic: GATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|58690350|gb|CK079037.1|CK079037
EST:     GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|88221933|gb|CI221889.1|CI221889
EST:     GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|86260924|gb|CI066599.1|CI066599
EST:     AGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: AGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|88830844|gb|CI079278.1|CI079278
EST:     ATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: ATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|33683327|gb|CF311566.1|CF311566
EST:     GTTCGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|88247112|gb|CI246961.1|CI246961
EST:     GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|88908200|gb|CI090795.1|CI090795
EST:     TACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: TACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
EST: gi|29633653|gb|CB638662.1|CB638662
EST:     GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAG                         GTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG
genomic: GTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATG

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 1 RNA-Seqlibrary.


Block sizes: 44 (upstream exon), 63 (downstream exon)
Score: 9

GATATGTCTATTGAACTGAGTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttt ... tggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcacctcactgcaaaaatatgtgaatggattactttgatttgtggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATGCAG
                                                ttttc  CT-rich tract
               aaaaatatgtgaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgtaaaaaaaaaagagtgaagggttatgattagacagaaagtgcatcacctcactgcaaaaatatgtgaatggattactttgatttgtggttttcagGTGGAGAAAATGATAGATACCACATACACTGCAAATATGAAATCAATGATGCAG

- - - aaaaaaa
- - - - - - - - - - - - - ttatgat
- - - - - - - - - - - - - - - - - - acagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaatg