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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG

Basic information

species Oryza sativa
transcript LOC_Os02g55150.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G178996_T01 (Zea mays), 3'ss of exon 5
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
|||  |||||| || |  |  |   |||||||| | ||| ||| || | || ||| | ||  ||| |   ||  |||||| ||| |||| ||||| || |||||||||||||||||||| || ||||||||||| || ||||||||| || ||||| |||                  
gtagtttagatctaatgctaga---tagatccatggtggttttattcttctcgctgacagc-tggagtaaaa--acagATACAACTGAAGGAGTTAGCAGAAGAAATGCAAGCGATAACTAAAGGACTGGAAAAAGTGGAGCAGGAACTGGCAACAGCTGAAAAGGATCCTTCAGAGA

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ37653 (Selaginella moellendorffii), 3'ss of exon 13
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
              ||  |  |    | |  | |  |   | ||| | | ||   |    ||||        | ||||||||||||||| |   | || ||||||||||||||  |||  ||||| ||||||||||||||||||||||||||| | ||||                  
-------------gttcttatatttcatactc-cagtatttgtgtctcggttttctgacctgtg--------ttacagATTCAATTGAAGGCTCTTGCAGAAGAAATGCAAGCCGTAAGCAAGGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCGTCTGAAAACGATGGAGCCGTCT

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 13
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
              ||  |      | |  |  |  ||  ||||| ||| ||   |   |||||        |  ||||||||||||||||   | || ||||||||||||||  |||  || || ||||||||||||||||||||||||||| ||||||                  
-------------gtttctatctttttgcacttcaatgtatttgtcttggttttctgacgtgtg--------tggcagATTCAATTGAAAGCCCTTGCAGAAGAAATGCAAGCCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCATCTGAAAACGATGGAGCCGTGT

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ38303 (Selaginella moellendorffii), 3'ss of exon 6
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------------------
                         || ||   |||   ||    ||||  |  |  |  | || |  ||  | ||||||||||||||| |   | || |||||||||||||   |||  || || ||||||||||||||||||||||||||| | ||||                              
--------------------gttcttatattt-cgtactctagtatttgtgtcttggttttctgatc-tgtgttacagattcaattgaagGCTCTTGCAGAAGAAATGCAAGTCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCGTCTGAAAACGATGGAGCCATCTCTGATGGGTTTC

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 13
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTG--GTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
                         |  |||    ||  |||   | |  |||  | | || |  ||  |||  |  ||||||||||||||||   | || ||||||||||||||  |||  || || ||||||||||||||||||||||||||| ||||||                  
----------------------gtttctatcttttttcacttcaatgtatttgtct-tggttttctgacgtgtgtggcagATTCAATTGAAAGCCCTTGCAGAAGAAATGCAAGCCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCATCTGAAAACGATGGAGCCGTGT

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ38305 (Selaginella moellendorffii), 3'ss of exon 10
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
              ||  |  |    | |  | |  |   | ||| | | ||   |    ||||        | |||||||||||||||||   | || ||||||||||||||  |||  || || ||||||||||||||||||||||||||| | ||||                  
-------------gttcttatatttcatactc-cagtatttgtgtctcggttttctgacctgtg--------ttacagATTCAATTGAAAGCTCTTGCAGAAGAAATGCAAGCCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCGTCTGAAAACGATGGAGCCGTCT

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ14916 (Selaginella moellendorffii), 3'ss of exon 9
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
                         || ||   |||   ||    ||||  |  |  |  | || |  ||  | ||||||||||||||| |   | || |||||||||||||   |||  || || ||||||||||||||||||||||||||| ||||||                  
--------------------gttcttatattt-cgtactctagtatttgtgtcttggttttctgatc-tgtgttacagATTCAATTGAAGGCTCTTGCAGAAGAAATGCAAGTCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCATCTGAAAACGATGGAGCCATCT

upper sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ15040 (Selaginella moellendorffii), 3'ss of exon 13
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG------------------
              ||  |  |    | |  | |  |   | ||| ||| ||   |    ||||        | |||||||||||||||||   | || ||||||||||||||  |||  || || ||||||||||||||||||||||||||| | ||||                  
-------------gttcttatatttcatactc-cagtatttgtgtcttggttttctgacctgtg--------ttacagATTCAATTGAAAGCTCTTGCAGAAGAAATGCAAGCCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCGTCTGAAAACGATGGAGCCGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG
           aattaac  putative branch site (score: 2)
                                       ttttgctt  putative PPT
     tatattaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttagatatattaattaacgctagatccacgttggctttgttttgcttgcttatagTGTGGTGGTGAATCACAGATTCAATTGAAAGAGTTGGCGGAAGAAATGCAAGCGATAACAAAGGGACTGGAAAAGGTTGAGCAGGAATTGACAACATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG