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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatag

Basic information

species Oryza sativa
transcript LOC_Os06g36090.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcat-cttgtcctgttccctgtc-------gtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatag
||| ||||||||||||| ||||| ||||||||||||||||||||| |  |||||  | |||||||||||| |||||||||||||||| ||||||||||| ||||||| ||||  |  ||   ||    |   | | |||||  || | |  |        | | ||    ||  ||  | |   |  |||| | || |  | || | | |  ||
TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttcttcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccag

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G366146_T01 (Zea mays), 5'ss of exon 10
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgatt--gagattaatgtttta-tacatag--------
||| ||||||||||| | ||    |||||| |||||||||||||| |  |||||  |||||||||||||| ||||||| |||||||||||||||||||| ||||||| ||||    | || |  |||  |||  || |||||| || | |  || | ||          |||||   |   ||   || | | |||    | | | | |        
TGGCAGCAATGAAGCCGCTCTGTCAAGAGGCATGGTTCTTCCATTCAACCCTCTTGCCATGTCTTTTGATAATGTGAATTACTATGTCGACATGCCTGCGgtgagttcacct----tcaattattctcagcaatttttcctgtcccatttgttaccttcctcaatgtgcttgtatcgtcaaatatggaaactgatggaaaactccgttgtttcccag

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G16340.1 (Arabidopsis thaliana), 5'ss of exon 12
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatag
    || ||      ||     | ||||||||||||||| || |||||||||||  | ||||| || ||  | || |||||||| ||||||||||||   || |    |   || |  ||    | ||| |||     ||       |||  || ||  ||  |||||                                      
AAAGAGTAAGAGCATTGACGTGAAAAGAGGAATGGTTCTACCTTTTACTCCTCTCACAATGTCCTTCGACAACGTAAACTACTACGTCGACATGCCTAAGgtaacaccaa--atcccaaatccttgttgacattaaaaccataaagatgt--taaccaaaaaagaaaacag-----------------------------------

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G15210.1 (Arabidopsis thaliana), 5'ss of exon 7
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatt-tgtaatatttgattgagattaatgttttatacatag
||  |   |    |   |  | |  | ||||||||||||||| || ||||||||| | ||||| ||||| ||||| || |||| ||| ||||||||||| || |   ||| |      ||  |   |   | | ||||  | ||     | | | |   ||  |||| |  | ||  ||| ||| | |                   
TGAGATGGAGAGTGTGAGCGCCAAGAAAGGAATGGTTCTTCCTTTCACTCCTCTAGCTATGTCATTTGACGATGTTAAATACTTTGTTGACATGCCTGCGgtaa---tactttga---aaactagttaaacttattgt--tattattaatagaaacaaaaaaagaaactcatatagaattggatggtgcag----------------

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g03560.t01 (Vitis vinifera), 5'ss of exon 4
TGGTAGCAA-TGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttt-tatacatag------------------
 ||  |||| ||  | || ||| | |||||||||| | ||||| || ||||| ||  ||||||| ||||| ||||||||||||||||| ||||||||  | || ||  | ||| | |||   |  | ||   | ||        |   | ||  ||    |||   | | | || |      | | |  | | ||     | |  ||                   
-GGCCGCAAATGGGGTTGCTCCCAAAAGAGGAATGATCCTTCCCTTCACTCCCCTCGCCATGTCCTTTGACGATGTGAACTACTATGTGGACATGCCACCGgtaagaatccctttcctttgttggtgttactacctacataacatggatttcaaatggagaattttagact-gtgaaggccaactaacttaactgccaacacaactaactctgttgatcataacag

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g03630.t01 (Vitis vinifera), 5'ss of exon 15
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatag
  ||   ||  || | ||    |  ||||||||| |||||||||||   |||||||||||||| |||||  |||| || |||||||| ||||||||    ||| ||||    |    ||           |||| || | |        |  | |    | |     | ||| |  |    | || | | | | |   |       
CAGTCCTAAGAAAACGGGCATTAAGAGAGGAATGATTCTTCCATTTTTACCTCTATCCATGTCCTTTGACAATGTAAATTACTATGTGGACATGCCCAAGgtgtgtttttagaaatctagaga-----aacatcatgactt--------tgatttagaaagttagctagttgaataacccaactgggctgattctaccag------

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 5'ss of exon 13
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttt-tatacatag------------------
||     ||||  | || ||| | |||||||||||| ||||| || ||||| ||  ||||||| |||||  |||||||||||||||| ||||||||  |||| ||  | ||| | |||   |  | ||   | |         |   | ||  ||    |||   | | | || |      | | |  | |  |     |||  ||                   
TGCCGCAAATGGGGTTGCTCCCAAAAGAGGAATGGTCCTTCCCTTCACTCCCCTCGCCATGTCCTTTGACAATGTGAACTACTATGTGGACATGCCACCAgtaagaatccct-tcctttgttggtgttactacccacataacatggatttcaaatggagaattttagact-gtgaaggccaactaacttaaccgccaacataactaaccctgttgatcataacag

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: 64 (upstream exon), 74 (downstream exon)
Score: 23

TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttac ... ttatacatagGAAATGAAGCAGCAAGGAGTGGTGGATGATAGGCTCCAATTGTTACGTGACGTTACTGGATCATTTAGGCCTGCAGTGCTGACAGCACTCATGGGAGTCA




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