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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttgtatttctggtttcaatgcagtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttctggctgctacatcat...

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 14
TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttgtatttctggtttcaatgcagtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttc-tggctgctacatcat--
|||||||||||| || || ||||||||||||||||| ||||||||||| ||| ||||||| |||    |   | |||||||   ||||  || |       |     |   || || | |   || |  |  ||  |   | ||  
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatattt-tatttcttgttgtggtcttggttttttc--attagtgtttcttaacgcgccaagacaatgacagttgtcaatgtgataccttatctttaatat

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttgtatttctggtttcaatgcagtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttctggctgctacatcat--------
|||||||||||| || || ||||||||||||||||| ||||||||||| ||||| | ||| |||  ||| |  | | ||| |||||||  || |   ||  | |  ||    |  ||||     | || |  || |||   ||        
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgt-tctcttgttgtaat-ctttatattttttgttagtgtttct--taacgatccaa----gataatgacagctgtcggcgtgataccctattttgtacc

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 12
TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttgtatttctggtttcaatgcagtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttctggctgctacatcat----
|||||||||||| || ||  ||||| |||||||||| ||||||||||| ||||| ||||| |||   ||   | |||||| |  ||||  || |   ||  |    ||  |  |  |  | |        | | ||  ||| |    
TGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTGgtaatatttgt-tttcttgttgttatcttgattttttttcattagtgtttct--taacgcgacaagacaac-gacagctgtcaatgtgatactttatctttaat

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 13
TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgta-atttttgtatttctggtttcaatgc---agtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttctggctgctacatcat
|||||||||||||||||| || |||||||| ||||| || ||||||  | | |    | |  || |||||     ||  ||   ||   |    || | |  || ||| |     ||| ||    || | |     |          
TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttcta--atggttct---tttgctaaaaattcttgttcatgtag--------

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|58695418|gb|CK084105.1|CK084105
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|218505577|gb|FG949556.1|FG949556
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|33794400|gb|CF323084.1|CF323084
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|14571277|gb|BI118645.1|BI118645
EST:     TGATCATGAAGGTGGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGG-AAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|58608873|gb|CK036906.1|CK036906
EST:     AGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCGGTGAAT
genomic: AGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|87012999|gb|CI297226.1|CI297226
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|58694362|gb|CK083049.1|CK083049
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|58668188|gb|CK056874.1|CK056874
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|38481573|gb|CF965662.1|CF965662
EST:     TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAAT

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: 64 (upstream exon), 66 (downstream exon)
Score: 40

TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttg ... tcaattacagGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttgtatttctggtttcaatgcagtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttctggctgctacatcat

- - - - - GGTGGA