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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaatctctctctctctcttgctggatggatctgctgctgcgcccctcccccgatctttccggcgagtccgccgacgagggcctcagatcttctc...

Basic information

species Oryza sativa
transcript LOC_Os09g06970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 2
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgta-aac---gaatctctctctctctcttgctg-gatggatctgctgct-gcgcccctcccccgatcttt--ccggcgagtccgccgacgagggcctcagatcttctc
|||| | |||||||||  || ||||| ||||||| || ||||| || ||||||||||||||||||||||||||||| ||||| ||||||||| | |||||||| |||    ||    | | | ||||  | |  | |  ||    | ||   |  ||    || | | ||  ||   || || | |  |   |      | ||     
TGGCAGTCTACTGCGGTGGCCTCTACACCGCCAAACCAGAGCTTGCTGCCCGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccagaaacaattttttttctcccgttatgttcaattctttactcaggttccaagtccaaaccttaaccaatga-tctgtcatcctag--tgtggttc-----

upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G123807_T02 (Zea mays), 5'ss of exon 2
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaac----gaatctctctctctctcttgctggatggatctgctgctgcgcccctcccccgatctttccggcgagtccgccgacgagggcctcagatcttctc
|||| | |||||||||  || |||| ||||||||||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||||||| | |||||||| |      ||    | | | |||| || |   |   ||  ||||      |  | | |    |    | | |  ||     ||| |  ||   | |     
TGGCTGTCTACTGCGGTGGCCTCTATGCCGCCAAGCCAGAGCTTGCTGCCCGCCGCATTGAGGCCATCGGCTTTCAGGTTGGGCACCAGCTCTCTGAGAGgtatagccagaaacaattttttttctcctgttctgttcttcatctgcctaattctgcactcaggttcctagtccaaaccttaaccgatgatctgtcaccc----

upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 5'ss of exon 1
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaatctctctctc----tctcttgctggatggatctgctgctgcgcccctcccccgatctttccggcgagtccgccgacgagggcctcagatcttctc
|||||   ||| | ||||| ||||| ||   ||||||||| |||||||| ||  | ||||||||||| || |  |||||||||||||||||| | |||||||        | ||   ||    |||  |   |    | |       ||   | ||     | |  |    |        | || || |    |  || |    
TGGCGATGTACAGTGGCCGATTCTATGCTAACAAGCCGGAACTCGCCGCTCGGAGGATCGAGGCCATTGGTTATCAGGTCGGCCACCAGCTCTCCGAGAGgtttgttttacacttgatcatcgtcttctttcgatctggttgatcattgtatctctaggttgctagtattagttgtagatctgaagatgatggcgaatgt----

upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 1
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaac-gaatctctctctctctcttgctggatggatctgctgctgcgcccctcccccgatctttccggcgagtccgccgacgagggcctcagatcttctc--
|| |  | || |||  ||| |||||||||| ||||||||| |||||||||||  | ||||| ||||| |||| ||||||||||||||||||| | ||  ||||  | |  ||||||||| |||||  ||  |     ||    || | ||         ||  ||            | ||       ||      || ||  
TGTCCTCGTATTGCACCCGTTTCTACGCCGACAAGCCGGATCTCGCCGCCCGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtctctctctctttctctctctaaac---cctataccttcaccttctgtttcattcttttcttatcatttctgattttctacttgtgggttttcaa

upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ20859 (Selaginella moellendorffii), 5'ss of exon 1
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaatctctctctctctcttgctggatggatctgctgctgcgcccctcccccgatctttccggcgagtccgccgacgagggcctcagatcttctc----------------------------------------------------------------------------
||||| | ||||||| | |  |  |  |  |||||||||| || ||||| ||||| |||||||| |||||||||||||| || || |||||| ||||||||||||      | |    |||   |||| |   |   ||  |||  |  |  |      |  |||| | |  || ||   |  | |       || | |                                                                             
TGGCGACTTACTGCGACAGGCTACATTCTTCCAAGCCGGATCTGGCCGCTCGCCGGATCGAGGCGATCGGCTTCCAGGTGGGACAGCAGCTCGCGGAGAGgtaaaa-----ttttctgctcaaatgcttgcgaggaatgtggct-tgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttctatcttttttcctctttccag

upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ32385 (Selaginella moellendorffii), 5'ss of exon 1
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaatctctctctctctcttgctggatggat--ctgc------tgctgcgcccctcccccgatct-----------ttccggcgagtccgccgacgagggcctcagatcttctc----------------------------------------------------------------------------
||||| | ||||||| | |  |  |  |  |||||||||| || ||||| ||||| |||||||| |||||||||||||| || || |||||| ||||||||||||  | | |||  |  |  | ||  |     ||   |||      ||  ||   | | ||  |||||           |||| | |  || ||   |  | |       || | |                                                                             
TGGCGACTTACTGCGACAGGCTACATTCTTCCAAGCCGGATCTGGCCGCTCGCCGGATCGAGGCGATCGGCTTCCAGGTGGGACAGCAGCTCGCGGAGAGgtaaa--attttcttacattgccgtggagctcaaatgcttgcgaggaatgtggcttgcattccttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttcgatcttttttcctctttccag

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|88340008|gb|CI650455.1|CI650455
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|58659704|gb|CK048384.1|CK048384
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|218488990|gb|FG968333.1|FG968333
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367807|gb|CI570546.1|CI570546
EST:     CGCCGCATCGAGG-CATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88740387|gb|CI763895.1|CI763895
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCAT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCAT
EST: gi|88367760|gb|CI570499.1|CI570499
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367809|gb|CI570548.1|CI570548
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88378526|gb|CI636473.1|CI636473
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88827123|gb|CI777688.1|CI777688
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88330158|gb|CI658463.1|CI658463
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATTCCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88825852|gb|CI776417.1|CI776417
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCT
EST: gi|88825407|gb|CI775972.1|CI775972
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367786|gb|CI570525.1|CI570525
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88569468|gb|CI660643.1|CI660643
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATTCCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88371498|gb|CI602676.1|CI602676
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|58685585|gb|CK074272.1|CK074272
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367769|gb|CI570508.1|CI570508
EST:     GCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCCTCACGGAGAG                         ATATAC-ATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: GCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGC-TCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367796|gb|CI570535.1|CI570535
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367759|gb|CI570498.1|CI570498
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|33814198|gb|CF332978.1|CF332978
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88570451|gb|CI661824.1|CI661824
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATTCCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|33813782|gb|CF332777.1|CF332777
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88367808|gb|CI570547.1|CI570547
EST:     CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT

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: 39 (upstream exon), 67 (downstream exon)
Score: 6

TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaat ... tcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGGCCTACTGCGGCCGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGCCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACGGAGAGgtaaacgaatctctctctctctcttgctggatggatctgctgctgcgcccctcccccgatctttccggcgagtccgccgacgagggcctcagatcttctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgacg