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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaatttgctcctcatgcctttttcag

Basic information

species Oryza sativa
transcript LOC_Os05g12490.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaat-ttgctcctcatgcctttttcag
  ||||  | || |||||| ||||||| | ||||||||| ||||| || ||||||||||||||||| || |||||||||||||||||||||||||| |||||| ||| || ||||  |   ||  ||    | | |  |||||  |    |||||| |   ||    || ||||||||||||
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagta-tatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 2
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaat-ttgctcctcatgcctttttcag
 |||||| | ||||||||| |||| |||| ||||||||||||||| || || || || ||||| |||||||||||||||||||||||||||||||| ||||||| |  || ||||  |   ||  ||    | | || || ||  | | ||||||||||  ||    || |||| |||||||
TTTACCATTACCAGAACTAGTAAAGTTTGCCTTTTTTGCAAACCTGTCGATCGTCGGAATGAACGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgagggcagaaactttggtattctataagta-tattggagttaaacgtatatactaatgctgtgtatcttgcccttttcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G27820.1 (Glycine max), 5'ss of exon 2
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagt--aactaagtcctttaatgttcacttttagaattggatgcatatactaatttgctcctcat-gcctttttcag
 |||||  ||||||| ||  ||||||||||  |  |||| ||| | || |||||||| |||||||||||| | ||||||||||| ||||||||||| || ||||     |   | ||   ||  ||   |||||  || |  | ||  | || |   |||| | | | |  | ||| ||  |||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCGTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgggctgagctttatctattg--gttca--ttcactaatgccttcagaagttaatattcactttttagccattgacag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G39590.1 (Glycine max), 5'ss of exon 2
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaaga-aagtaactaagt--cctttaatgtt------cacttttagaattggatgcatatactaatttgctcctcatgcctttttcag-------------
  | |||||  | ||  |||| ||||||||||| ||||||||  | || ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||| |    |||    | |||  ||| |||  ||      |   |||| |||    |  | |||   ||||  |  | || | |  || |              
TCTTCCAGTATCTGATATAATCAAATTTGTCTTATTTGCAAATTTCTCCATTGTTGGGATGAATGTGAGTTTAATGTGGAACTCTGTTGGTTTCTATCAGgtaactttaaggcttttagtagcctataacattttgaaccgtctttataataaactaaagataaatattta-taataattcttccttgaaattaaattgtcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G08700.1 (Glycine max), 5'ss of exon 3
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcct--ttaatgttcacttttagaattggatgcatatacta-atttgctcctcatgcctttttcag
 |||||  ||||||| ||  ||||||||||  | ||||| ||| | || |||||||| |||||||||||| | ||||||||||| ||||||||||| || ||||     |   || ||   |   || || | | ||  |  | ||  | || |   || |||  ||  | | ||| ||  |||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCTTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttggg---ctgagctttatctattggttaattc-attaatgccttcagaagttatattcacttttta-gccattgacag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G15250.1 (Glycine max), 5'ss of exon 2
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtccttta---------atgttcacttttagaattg-----gatgcatatactaatttgctcctcatgcctttttcag--------------
| | ||  | || || || || ||||||||||| ||||||||  | || ||||| || |||||||| |||||||||||||||||||| || ||||| ||||| |  |   ||  |   |  ||||          | |  | |||||  | ||     ||   | |||   ||||   |    | | |  ||                 
CCTTCCCTTACCTGATCTTATCAAATTTGTCTTATTTGCAAATTTCTCTATTGTCGGCATGAATGTGAGTTTGATGTGGAACTCTGTCGGTTTCTATCAGgtaacaactatattttttttttttatctttgaaagtatcaagttttaacactgccagtgacaaagataggtatttatactgtttccttcctttgaaatgaaaacttcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G31940.1 (Glycine max), 5'ss of exon 4
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaacta--agtcctttaa---tgttcacttttagaattg-----gatgcatatactaatttgctcctcatgcctttttcag--------------
| | ||  | || || || || ||||||||||| ||||||||  | || ||||| || ||||| || |||||||||||||| ||||| || ||||| ||||| |  | | |   ||  | |  ||| |   | |  | |||||  | ||     ||   |  ||   ||||        | | | | |                 
CCTTCCCTTACCTGATCTCATCAAATTTGTCTTATTTGCAAATTTCTCTATTGTCGGCATGAACGTGAGTTTGATGTGGAATTCTGTCGGTTTCTATCAGgtaactagattttttacaaattttttgaaagtatcaaattttaacactgccagtgacaaaggtaggtatttatagtgtttccttctcttgaaatgaaaacttcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G15280.1 (Glycine max), 5'ss of exon 3
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaaga-aagtaactaagt--cctttaatgtt------cacttttagaattggatgcatatactaatt-tgctcctcatgcctttttcag----------
  | ||| |  | ||  |||| ||||||||||| ||||||||  | || ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||| |    |||    | |||  ||| |||  ||      |   |||| | |    |  | ||| || || |  |  | || ||||                
TCTTCCATTATCTGATATAATCAAATTTGTCTTGTTTGCAAATTTCTCCATTGTTGGGATGAATGTGAGTTTAATGTGGAACTCTGTTGGTTTCTATCAGgtaactttaaggcttttagtagcctataacattttgaaccctctttatagtaaactctagataatatttataataattattccttgaaataaaattgtcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G36620.1 (Glycine max), 5'ss of exon 2
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttc--acttttagaattggatgcatatactaa-tttgctcctcatgcctttttcag
 |||||  | ||||| ||  |||||||||| || ||||| ||| | || |||||||| |||||||| ||| | ||||||||||| ||||||||||| || ||||      |    |  | |  || || ||  |  |  |  | || || || |   ||| ||| || || |  || ||  |||
TTTACCCTTACCAGAGCTTCTAAAATTTGTTTTCTTTGCTAACTTCTCCATTGTTGGAATGAATGTCAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgtattga-attttcactattggtccaaggtccattaatgcattcagaagttaaattttcttctta-accattggcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 5'ss of exon 3
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggat-gcatatacta-atttgctcctcatgcctttttcag
  | ||  |  | || ||  | | |||| |  | ||||| ||  | || |||||||| |||||||| ||| | ||||||||||||||||| || || |||||     |  | |   ||  || ||||  | |     |||| || || ||  ||  ||   |||  |    |    || ||||
TCTTCCGTTTACGGAGCTTTTGAGATTTATTCTGTTTGCTAATTTCTCCATTGTTGGAATGAATGTCAGTCTTATGTGGAACTCTGTTGGTTTTTATCAGgtattagacatcatctagctctgtaattgtga---aaagaaatgtattgctgattttatgattgtcctgtttttgcttgtcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G39390.2 (Arabidopsis thaliana), 5'ss of exon 3
-CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagt---aactaagtcct--ttaatgttcacttttagaattggatgcatatactaatttgctcctcatgcc--tttttcag--------
 ||| |  | ||| || ||  | ||||| || || || || ||| | || || ||||||||||| || ||| | |||||||| |||||||| |||||||||||        |   | ||   | |   || | |||  | ||     ||  | |  | |  || |  | || | |  |   | | |  |        
GCTTCCTTG-GCCTGATCTTTTGAAATTCGTTTTGTTCGCTAACTTCTCTATCGTTGGGATGAACGTCAGTCTCATGTGGAATTCTGTTGGCTTCTACCAGgtctgtcctttttcatctcgatgcggatttacgttttccttc---gtttaaagttttttttagtaagatcttgaaacgagtgtgttggcattgcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaatttgctcctcatgcctttttcag
  | ||| |  |||| ||  | || ||| |  | ||||| ||  | || |||||||| |||||||||||| | ||||||||||||||||| || || ||||| ||     |  ||   |   |||     |  || | |   | | | |  ||  |   ||     | ||||  ||  |||
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgc--ttaacag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 5'ss of exon 2
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaag-taactaagtcctttaatgttcacttttagaattggatgcatatactaatt-tgctcctcatgcctttttcag
  | ||  | ||||| ||  | |||||||| || ||||| ||| | || |||||||| |||||||||||||| ||||||||||| || || ||||| |||||  |    | |  ||  ||   || | | | || |||  | |   ||   |  |  | ||      || ||     | ||||
TCTCCCCCTTCCAGAGCTTCTGAAATTTGTATTATTTGCGAACTTCTCTATTGTTGGAATGAATGTTAGTTTAATGTGGAACTCAGTAGGGTTCTATCAGgtatattctgattgctctgtgtgtttaagcttacatttt-attgtaataattgcagaagttacatctctaatttaactgtcag

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 3
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattgg-atgcatatactaatttgctcctcatgcctttttcag-----------------
  |||||||  | || ||  | | |||||| || ||||||||  | ||||||||||| ||||| || ||||| |||||||||||||| |||||||| ||||| |     |  |     |   ||  ||||| | ||| |   |   ||   | | | || || |   | |||   |||                     
TCTACCAGTATCTGAGCTTCTGAGATTTGTTTTGTTTGCAAATTTGTCAATTGTTGGAATGAACGTGAGTTTAATGTGGAACTCTGTGGGATTCTATCAGgtcagttttgggaactgctgactttttgttctccttttgctctcatattttttttcaaagttacaagttatgttctttctcttcaaactttgatgtcag

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: 66 (upstream exon), 64 (downstream exon)
Score: 14

CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaag ... cctttttcagATTGCCAAGTTATGCATCATTCCAGTTTTGTGCTTTCTGGAAATCCTGTTTGATAAAGTCCGATACTCAAGAGATACAAAGTTCAGTATAATGGTTGTTC




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