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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactgttcgcaatggttgctgtccatctctatgaaaagattagctctattacatgggtgatacccggtactctgttaagtcctgttgtttttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G130749_T01 (Zea mays), 3'ss of exon 12
-atactgttcgcaatggttgctgtccatctctatgaaaagattagctctattacatgggtgatacccggtactctgttaagtcctgttgtttttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
 |     |   |    | |||| |   |   |||  |    |  |  || |||         |     ||  |    | | |  || |  |||  || |||||||||||||| || ||||| ||| |||||||||| ||||| ||||||
tagctcctatactgaaggtgctatattttgttatccagtcttctgtgctgttattattactgtttaaagttattcacttatttgtgctagtttg-ttacagGAAGTTGCTGTTTTTATATCGTTCTTTGTTTCTGCTGTACTTCATGAG

upper sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G130749_T02 (Zea mays), 3'ss of exon 12
-atactgttcgcaatggttgctgtccatctctatgaaaagattagctctattacatgggtgatacccggtactctgttaagtcctgttgtttttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG----------------------------------------------------
 |     |   |    | |||| |   |   |||  |    |  |  || |||         |     ||  |    | | |  || |  |||  || |||||||||||||| || ||||| ||| |||||||||| ||||| ||||||                                                    
tagctcctatactgaaggtgctatattttgttatccagtcttctgtgctgttattattactgtttaaagttattcacttatttgtgctagtttg-ttacagGAAGTTGCTGTTTTTATATCGTTCTTTGTTTCTGCTGTACTTCATGAGGTAACTTATTTACCTTTTCACTCTTCATCTGCTATATTAATTATATAGTTCT
















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|29664361|gb|CB660636.1|CB660636
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29615462|gb|CB620474.1|CB620474
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29664325|gb|CB660600.1|CB660600
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|25803480|gb|CA759449.1|CA759449
EST:     GTATATCAAAG                         GAAG-TGNCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTG-CTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29641508|gb|CB646515.1|CB646515
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29664362|gb|CB660637.1|CB660637
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29646484|gb|CB651491.1|CB651491
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|88520579|gb|CI448233.1|CI448233
EST:     GGGTTGTTCCCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAA-Ggtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29614065|gb|CB619078.1|CB619078
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|66928227|gb|CX115075.1|CX115075
EST:     GGGTTG-TCGCCATA-TTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
EST: gi|29615460|gb|CB620472.1|CB620472
EST:     GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAG                         GAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
genomic: GGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG

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: 63 (upstream exon), 48 (downstream exon)
Score: 17

CCTGTACATAAATGGGTTGTTCGCCATATTTACTTTCCTTGCATGCGAAATGGTATATCAAAGgtaaaacttc ... tttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattacatgggtgatacccggtactctgttaagtcctgttgtttttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG
                                   tcctgttgtttttctt  CT-rich tract
                                           tttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atactgttcgcaatggttgctgtccatctctatgaaaagattagctctattacatgggtgatacccggtactctgttaagtcctgttgtttttctttcagGAAGTTGCTGTCTTGATATCATTCCTTGTTTCTGCCGTACTCCATGAG

-tactgtt
- - - - - - - - -tgctgtc
- - - - - - - - - - - - - -ctctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgt