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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcagaatcttg...

Basic information

species Oryza sativa
transcript LOC_Os08g31840.4
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g31840.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 6
CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcagaatcttg----------------------------------------------------------------------------------------
                                                                                        ||| |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||| || || |||||||| ||||||||                                                                                         
----------------------------------------------------------------------------------------AAACCCAAGCATGTATGCAAGTCAATGGTTTATCACAGTTTTCTCATATTCCTTCCCATTTCATCTAACTCTTAGAGTTTGGGATGTGTTTCTTTATGAGgttagaatcttatcctgccatatgtgcattttgtgtttagattgcaccttgggttatttgacttttctttatgcactattgcttcataaatggtatagtc

upper sequence: LOC_Os08g31840.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G07090.1 (Glycine max), 5'ss of exon 5
CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcag--aatcttg------------------------------------------------------------------
                                                                                        |||||| ||||||||||| || || ||||| || |||||||| ||||| ||||| || |||||| |  ||||| || ||||||||||||| || |||||||| ||  |  |||                                                                   
----------------------------------------------------------------------------------------AAATCCTAGCATGTATGCTAGCCAGTGGTTCATAACTGTTTTTTCGTACTCCTTTCCATTTCATTTGGCTCTTCGAATTTGGGATGTCTTTCTCTATGAGgttagctatgctttccatttgaagaaccatttattggttagaaatatggacctataatgatgactttcttatccttccag

upper sequence: LOC_Os08g31840.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA19G05360.1 (Glycine max), 5'ss of exon 6
CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcagaatcttg----------------------------------------------------------------------
                                                                                        |||||| ||||||||||| || || ||||| || ||||| || || |||||||| || |||||| |  ||||| || |||||||||||||||| || ||||| ||  |  ||                                                                      
----------------------------------------------------------------------------------------AAATCCTAGCATGTATGCTAGCCAGTGGTTCATAACTGTATTTTCATATTCCTTTCCATTTCATTTGGCTCTTCGAATTTGGGATGTCTTCCTCTACGAGgttag--ttgtgctttccctctgaagaaccatttattggttagagatatggatctataatgatgactttcttatcattccag

upper sequence: LOC_Os08g31840.4 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 6
CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcagaatcttg-------------------------------------------------------------------
                                                                                        ||  || ||||||||||||||||| ||||| || ||||||||||| || || ||||| || ||| |  ||||| || ||||||||||||| || |||||||| ||     |                                                                    
----------------------------------------------------------------------------------------AAGCCCTAGCATGTATGCAAGTCAGTGGTTCATAACTGTTTTCTCATACTCTTTCCCATTCCATTTGGCTCTTCGAATTTGGGATGTCTTTCTTTATGAGgttagtggtctaaaagctcattaaattctccaataggcaccattattttgttttaggaacatttttattccttgggcag

upper sequence: LOC_Os08g31840.4 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S15_13V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCTTGTGCAGCAATATCTGTATCAGTT--TGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgta--tgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtat-gaggtcagaatcttg
            |  || | |   |||   ||    || |         || |  ||     |    |   |  |    | |     |||   | |   || |    | |  |   |   ||  || |  |||   |   |   | | | | | ||  | || |   |  |   | |    || ||||  || ||| | ||  | 
-----AAATCCAAGCATGTATGCTAGTCAATGGTTCATCACCGTCTTTTCATACTCCTTCCCTTTCTCCTTAGCTCTGCGGATTTGGGATGTGTTCTTACACGAGgtttcttgcttactcttcctctccctttcagcagctctttacacgtgttatgcatctttgcaatgtccagttcatgtcttgtagagaagtctggataatc

upper sequence: LOC_Os08g31840.4 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ27331 (Selaginella moellendorffii), 5'ss of exon 5
CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcagaatcttg------------------------------------------------------
                                                                                        ||| ||||||||||| || || || ||||||||||||||||| || |||||||| || || |  ||| ||||| |  | ||||| || || ||||| |||||  | ||||                                                        
----------------------------------------------------------------------------------------AAACCCAAGCATGTACGCCAGCCAGTGGTTTATCACTGTTTTTTCTTATTCCTTTCCGTTCCCGCTAGCTCTTCGGATATGGGACGTTTTTCTGTACGAGgtttgtatctctttcttgcttatctatttttttctgaagagttgcgaggctgctattatgttgcag

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|88521174|gb|CI448836.1|CI448836
EST:     CATTTTATTGAAGAAATGATAAATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: CATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88545457|gb|CI475019.1|CI475019
EST:     GAAATGATAAATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: GAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88534582|gb|CI463316.1|CI463316
EST:     AATGATAAATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: AATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88522486|gb|CI450250.1|CI450250
EST:     TTGGGACAGCATTTTATTGAAGAAATGATAGATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGAGTGGCTCTATTGAGATTTTGCCAT
genomic: TTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88522709|gb|CI449545.1|CI449545
EST:     GCATTTTATTGAAGAAATGATAGATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: GCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88548655|gb|CI476470.1|CI476470
EST:     ATTTTATTGAAGAAATGATAGATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: ATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88539072|gb|CI468151.1|CI468151
EST:     GACAGCATTTTATTGAAGAAATGATAAATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: GACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
EST: gi|88521569|gb|CI449270.1|CI449270
EST:     TTTTATTGAAGAAATGATAAATCCAAGCAT                         GGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT
genomic: TTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagt ... ttatctacagGGCATTAAGGTTGTATTCCAAGTTGGATTGGCTCTATTGAGATTTTGCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTTGTGCAGCAATATCTGTATCAGTTTGAGAAATTAGTTCTGGAGCAAATGCCACAGTTGGGACAGCATTTTATTGAAGAAATGATAAATCCAAGCATgtatgcaagtcaatggtttatcactgttttctcgtattccttcccttttcatctaactcttagagtttgggatgtcttcctgtatgaggtcagaatcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttccc