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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgctaaataaattatctgtcctgcgatgttgcttccacaacttgaaatccttggtattaatatgtaactatgtctcgtatgggggttgaaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAACTGCATTATTGAGTACATTAGACCATGAATCTAGTGTCAAAGACAGCTGG

Basic information

species Oryza sativa
transcript LOC_Os06g20320.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g20320.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G127393_T02 (Zea mays), 3'ss of exon 12
--catgctaaataaattatctgtcctgcgatgttgcttccacaacttgaaatccttggtattaatatgtaactatgtctcgtatgggggttgaaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAACTGCATTATTGAGTACATTAGACCATGAATCTAGTGTCAAAGACAGCTGG
  |  |||   |    | | || ||| |     |    | ||| | |       ||   |     |||    | | | ||     | | || ||  |||||||| |||||||| |||||||| ||||||||||| |||||||||||||||||||||    | ||||| || || | |||| ||    |     |      ||
gtctggctgtttctggt-tgtgacctcctccactaaa-ctacagcctagctctgttctcacactcatgcgtatgtatttctacgcgcgattcaatgatgcagGTCCAGGATGTCCTAGAGGCGGCGAAGGTGCTTGAATGGCTCAAGGAGAACTGCTCGGTCGAGTATATCAGGCGATGAGTCCCACGATGCTGGGTCAAGG
















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|29664069|gb|CB660344.1|CB660344
EST:     AGTTCAAACCCTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|86259623|gb|CI065496.1|CI065496
EST:     AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|22307622|gb|BQ908844.1|BQ908844
EST:     AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTCGCTCGAATGGCTCAAGGAGAA
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGT-GCTCGAATGGCTCAAGGAGAA
EST: gi|88956490|gb|CI092736.1|CI092736
EST:     AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|3767819|gb|AU031846.1|AU031846
EST:     AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|88476941|gb|CI414212.1|CI414212
EST:     AGTTCAAACACTATAATCAAGGCTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|25806488|gb|CA762449.1|CA762449
EST:     AGTTCAAACCCTATAATCAAGACTTTGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|87006864|gb|CI285898.1|CI285898
EST:     AGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
EST: gi|86852956|gb|CI323265.1|CI323265
EST:     AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAG                         GTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC
genomic: AGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAAC

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: 69 (upstream exon), 73 (downstream exon)
Score: 27

TTTTCGACCGAGCAACTGGTAAAGGAAGTTGAGAACTCTATAGAAGAGTTCAAACACTATAATCAAGACTATGATGAGGGGAGCATCAAGCAGCAGgtttttaact ... aaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAACTGCATTATTGAGTACATTAGACCATGAATCTAGTGTCAAAGACAGCTGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatccttggtattaatatgtaactatgtctcgtatgggggttgaaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAACTGCATTATTGAGTACATTAGACCATGAATCTAGTGTCAAAGACAGCTGG
           tattaatatgtaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgctaaataaattatctgtcctgcgatgttgcttccacaacttgaaatccttggtattaatatgtaactatgtctcgtatgggggttgaaccatgcagGTTCAGGATGTTCTAGAGGCAGCGAAGGTGCTCGAATGGCTCAAGGAGAACTGCATTATTGAGTACATTAGACCATGAATCTAGTGTCAAAGACAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
catgcta
- - - - - - - - - -gtcctgc
- - - - - - - - - - - - - - - -tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atatgta