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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacag

Basic information

species Oryza sativa
transcript LOC_Os01g01710.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 8
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtt-tgcagta--aactttc-----agaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacag
||||| | ||||||| |||||||||||||| ||||||||||| || |||||||||||||| | |||||| || |||||||||||||| ||||||||||||||||  |  ||    | ||||      | ||   |  | |   ||| ||     | |   ||||||| |||  ||||| |   |  ||
TGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcatagagctccatcttttttgaaaaaaaaatctttaatccatatttattat-taaacactaaattgacgacttggtct-tgtag

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G036290_T01 (Zea mays), 5'ss of exon 8
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgt-ttgcagta--aactttcagaattttactgaggtcatgttggcagtatttg-cactaaaatgatcacttgattcatacag
||||| | ||||||| |||||||| ||||| ||||||||||| || |||||||||||||| |||||||| || |||||||||||||| |||||||||||||||| ||  ||    | ||||   || | |  | |   | | ||     | ||   ||||||| |||  ||||| |   |  ||
TGACAGGCTGAAAGATGTAAAAGTAGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAAGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcttagagctccagcttttttaaatgtgtttaatccttatttattatgttaaacactaaagtgacaacttggtat-tgtag

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 8
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacag-----------------------------------------
||| ||  ||||||| || |||||||||||||| ||||| || || ||||||||||||||||| ||||| ||||| || ||||||||  | || || ||||| |     ||    |||   |  |  ||  |    | |     ||  |||  |  ||  || | | ||   |  ||                                            
TGATAAACTGAAAGATGTTAAAGTTGCTGATGCATTAAAACATCCTAACTGGAATATGGGGAAAAAGATAACTGTGGACTCTGCTACCCTTTTTAATAAGgttt-----gtttctttttttatgtcaacatattggacgcaaatagcctttttataaatctgtttaattatgtggtatgaatttcctagctataaggtaaatttcttatacttcttcacag

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 8
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacag-------------------------------------
||| ||  ||||||| || |||||||||||||| ||||| || || ||||||||||||||||| ||||| ||||| || ||||||||  | || || ||||  |||||  |    |||     |  || |||    |    | || | | |  |      | || |  || |    |                                        
TGATAAACTGAAAGATGTTAAAGTTGCTGATGCATTAAAACATCCTAACTGGAATATGGGGAAAAAGATAACTGTGGACTCTGCTACCCTTTTTAATAAGg--tttgc--ttctttttttatgtcatattgaatgaaaagagccattttataaatctgtttaattatgtggtatgaatttcctagctataaggtaaatttcttctgcttcttcacag

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 8
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgc--actaaaatgatcacttgattcatacag----
 || ||| | || ||||| ||||| || ||||| || ||||| || |||||||| ||||| ||||| || ||||| || ||||||||  | |||||||||||        |   ||   |   ||  |||  | |  ||     |   ||     |   | ||||   |||||||  |  |     
CGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACGCTTTTCAACAAGgttaagattattttctcctaaggttaaactctgattttgaaaatacctttgatcaaggtagatgagttcttgattttttgaaacag

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 8
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcact-tgattcatacag------------------------------
||| || ||||||||||  |||||| | |||||||| ||||| || ||||||||||||||||| ||||| || || || || |||||  | ||||| ||||| | | |  |      |     | ||  |||   ||||    || ||| || |  ||  |  ||||| || |       |                              
TGATAAATTGAAAGAAGCTAAAGTTTCAGATGCTTTGAAGCATCCTAACTGGAATATGGGGAAAAAGATCACGGTTGACTCAGCTACCCTTTTCAATAAGgtttgtcccttttttggtgtctctattcttgattacatgc-accaatatgtgaatgaatctactcactatggtctgagttgcaacaaataccttgttttcctttttgacag

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|86898927|gb|CI296156.1|CI296156
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTACGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGA
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTA-GAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGA
EST: gi|29613665|gb|CB618678.1|CB618678
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|29620640|gb|CB625651.1|CB625651
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|29688465|gb|CB684740.1|CB684740
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|58674748|gb|CK063435.1|CK063435
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|29620627|gb|CB625638.1|CB625638
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|58696138|gb|CK084825.1|CK084825
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|58694512|gb|CK083199.1|CK083199
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|38475522|gb|CF959655.1|CF959655
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|29617050|gb|CB622062.1|CB622062
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|58594695|gb|CF993003.1|CF993003
EST:     GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATAGGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
EST: gi|58595068|gb|CF993376.1|CF993376
EST:     GGAATATGGGGAAGAAGATTACTGTAGATGCTGCTACATTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC
genomic: GGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGAC

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: 63 (upstream exon), 74 (downstream exon)
Score: 41

TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcag ... attcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAAGTTGAAAGAAGTAAAAGTTGCTGATGCTTTAAAGCACCCGAACTGGAATATGGGGAAGAAGATTACTGTAGATTCTGCTACATTATTCAACAAGgtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG