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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcaagctctcaacttatggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcagGGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTATGTGTAGTACCCCCTAGTTCCTCGATTGCTACAAAGAAA

Basic information

species Oryza sativa
transcript LOC_Os12g35350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G174830_T01 (Zea mays), 3'ss of exon 11
gtatgtttcaagctctcaacttat--ggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattata--gcagtttgtaacaaaaaatatcgaattctcagGGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTATGTGTAGTACCCCCTAGTTCCTCGATTGCTACAAAGAAA
||| || ||||||||||     ||  ||||   || ||||  ||      ||||||    ||      ||||  ||    ||   ||  |||    |||| | || |   ||| ||| |||||| ||||  | |||||||||| ||||| ||||| |||| |||||||||| || ||| ||| ||||| || |||||||| ||||||||||| |||||| ||||||| |||
gtaagtctcaagctctctctcaatttggaagatgagttggtgat-----ttatttcttaatg-----aagaatacatgtattgctaatgatgacc-atctagcttcttttgcaatttctaacaagaaat--caaattctcagGACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTTGTGTAGTGCCCCCTAGTTCATCGATTACTACAAAAAAA
















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|300215852|gb|HO088478.1|HO088478
EST:     TCTATGTGGAACT-AGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAAC                         GGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTAT
genomic: TCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttca ... gaattctcagGGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcagGGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTATGTGTAGTACCCCCTAGTTCCTCGATTGCTACAAAGAAA
                            ttgtaac  putative branch site (score: 2)
                                                ttctc  putative PPT
                           tttgtaacaaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcaagctctcaacttatggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcagGGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTATGTGTAGTACCCCCTAGTTCCTCGATTGCTACAAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA