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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA

Basic information

species Oryza sativa
transcript LOC_Os12g30540.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 2
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
                               ||   ||||  |     |   ||| ||   | | |  |  |   | | || | | | | |     || |||||  |||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| || |
-------------------------------gtaacattctttatgacaaatgtt-cattcaatacaatacttgcggacttgtattaactttcctcttatttcttctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACGCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGA

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 12
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtgg-ttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
     |   | | || |||||  |||||| | | |||| || | | ||   |  ||| |  ||||| || | | |||               ||||  |  || |  |||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||  ||||||||||
----gtaaaattctttataacaattcattcaatacaatacagttacttgaggacttgtataaattttccacttattg---------------cttaact-cttattctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACACCATTCAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTATATACGTGAGAATGACAAGGATA

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 8
--------------gtcgtttttactattaataactgttcattaagtgca-attcactgatttagtggttgcagcaatttc--cctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
              |   || ||    ||      | |   ||   | || |||   ||| || ||           |||   | ||||| ||   || | |  | |  | ||||  || |  ||| | |  ||||||| |||   ||||| ||||| ||| |  || | || |||| ||| |||||  | |||||||| || |||||||||||| | |||||||| ||||||||||
gtaatactcagtaagcatttgttgggcttgtctcttatgttttttcttcatatttgttgacttggtaaagattttcttttggacatcatcatggtcttttttgtttacttcattttatttttattttgtt--aacagTTACCTTGTATAAATCCTGGCTTCGACCACTCTCCTTTTAGATTTACAAAACACTCGAATGCATATATGCTTGTCTATGTACGTGAGAGTGACAAGGATA

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACA---CCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
                               ||   |||  ||   |   |  || ||  | ||   | |   |  || ||     | |  || |  | |||   ||   |      ||| | || || |  || |||||||||||||| |   | || || |||||||||||||| |||||||| ||||||||||| ||||| || || || ||||| |   
-------------------------------gttttattttcttgctccatt-ttccatgatttgaaccccaatcctaattcctctagc--ctgacatatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 12
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
                                 | |   | ||  ||| | ||||      |||| | |  |  | | ||| |       |    ||    | |  |||   |    ||||| || || |  || ||||||||||||||  | || || ||||||||||| || |||||||| ||||||||||| |||||||| || || ||||||||||
---------------------------------gtagcactctc-tttcgaggttttctttattttctttgttatttttttttactgaatttactttcaaatttggtttctct---tcagTTACCGCAGAATAATCCTGGTTTCAATAATCCACCTTTCAAATTCACAAAATACTCGAATGCATACATGCTTGTTTATATTCGGGAAAGTGACAAGGATA

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctctt--ttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
                             | ||      || || |||  |   | |  ||| ||   || |   ||| || |||  | ||||  ||   ||||| |  ||| ||| |||||||||| || | ||||||||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||||| ||||| ||||| || |||||||| |
---------------------------gcatgtctttaccagtg-tttctttactccgtcaactttattc-ttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
gtcgtttttactattaataactgttcattaagtgcaattcactgatttag----tggttgcagcaatttccct-catcttgtatttatgtcatcatcttatttgtttctcttttggatgg--aacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
                 |||   ||  || |||  |  |||    ||| |    |  |||      ||  | | ||| || | |  |  ||||  | ||   |  ||  | | |  |||   ||||| |||| || | ||| ||||| || ||||||||||| |||||||| || |||||||| ||||| |||||||| || ||||| ||||| || |||||||| |
----------------gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 12
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
                 ||| |  |    |||   |  |      |||  |   | |    ||||   | ||||| |  ||||  ||  ||  ||| ||| |       | ||  ||||| | || || | ||| || || ||||| ||| | ||||| ||||| ||||| || || ||||| ||||||||||| ||||| ||||| || |||||||| |
----------------gtaatttattcacaagcatagattgtaagttttctttctacttttattt---taatcttattcttat--caatattatatctgtct-------gtatccaacagCTACCCCAGACAAATCCCGGATTCAACAACTCTCCATTCAAATTTACAAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

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|88995585|gb|CI022908.1|CI022908
EST:     AAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAG                         TTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAG
genomic: AAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAGgtcgttttta ... gatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAG
EST: gi|88275694|gb|CI396298.1|CI396298
EST:     AAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAG                         TTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAG
genomic: AAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAGgtcgttttta ... gatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAG

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: 74 (upstream exon), 74 (downstream exon)
Score: 45

GTATAAATTTGATGATGAACGAGTAACAAAAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAGgtcgttttta ... gatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA
        ttgtatttat  TA-rich tract