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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgaaattctcaaactacaattattcatatcatactttacatgactgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG

Basic information

species Oryza sativa
transcript LOC_Os02g01100.1
intron # 8
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G134888_T01 (Zea mays), 3'ss of exon 8
----acgaaattctcaaactacaattattcatat-catactttacatga--ctgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG
     ||   |  |||  | |       |   || ||   |||||   |  || | | |||||   |||| | ||    |  |       ||||||  ||||| |||||||||||| || || |  |||||||||||||||||||||||  ||||||| ||||| || || |||||| | |  ||||||||||||||||| || |||
acagtcgggttcttcattccattgaggataccatacacgttttactacatcctcagattattgca-atattgttcgcttactt------tccttaatgaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG

upper sequence: LOC_Os02g01100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G105192_T02 (Zea mays), 3'ss of exon 7
acgaaattctcaaactacaattattcatatcatactttacatgactgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG--
                |   ||  | ||||    ||    |   ||     | |  ||   ||   | |   |  |   ||  ||||||| |||||||||||||||||| |||||||||||| || |||||||||||||||| ||||| || |||||||| ||||||||  | |||||| |||||||||||||  |||||  
----------------atcctttcttatatttggctgggtaattctttgtttttcatg---atacttgtcaaactttctatgtccttaacgaataatcacatATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTGGT

upper sequence: LOC_Os02g01100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G105192_T03 (Zea mays), 3'ss of exon 7
acgaaattctcaaactacaattattcatatcatactttacatgactgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG
               ||   ||  | ||||    ||    |   ||     | |  ||   ||   | |   |  |   ||  ||||||| |||||||||||||||||| |||||||||||| || |||||||||||||||| ||||| || |||||||| ||||||||  | |||||| |||||||||||||  |||||
--------------atatcctttcttatatttggctgggtaattctttgtttttcatg---atacttgtcaaactttctatgtccttaacgaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG

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|86498766|gb|CI141399.1|CI141399
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatccttgg ... aaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
EST: gi|27548100|gb|CA766182.2|CA766182
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatccttgg ... aaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
EST: gi|29659581|gb|CB655856.1|CB655856
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatccttgg ... aaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
EST: gi|29678444|gb|CB674719.1|CB674719
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatccttgg ... aaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
EST: gi|87006659|gb|CI295042.1|CI295042
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatccttgg ... aaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
EST: gi|29663318|gb|CB659593.1|CB659593
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatccttgg ... aaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG
                                    acccttaac  putative branch site 
                                        ttaacaaataatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgaaattctcaaactacaattattcatatcatactttacatgactgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT