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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattttcagctgtaagagttcagctttgatgtaaactgttggcctaatacatttgctgtttcag

Basic information

species Oryza sativa
transcript LOC_Os12g01390.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 11
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattttcagctgtaagagttcagctttgatgtaaactgttggcctaatacatttgctgtttcag
||| |||||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| || |||||||||||||||||||||| |||| |  |      || |    | |||| || | ||         | ||||  |    ||||  ||                    
TGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATACTTATATATTCAAAGCAGgtatgtttgctttggttatgtggaagtccttttttagttata----cctgaccttgaact--tttgttttccag------------------

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttc-agtactgatgaatcctcat----tttcagctgtaag-----------agttcagctttgatgtaaactgttggcctaatacatttgctgtttcag-----------
|||  ||||||| || || || ||||| || || || ||||||||||| |||||||| || || ||||||||||| |||||||| |||||||| |||||||||| ||| ||| |||   |  ||||| | |     ||   | ||| |            |  | || |||  |  | ||| |    || ||| |||   |  ||              
TGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCCTGATATATTCTAAGCAGgtattttttttctagtttagtagaatcataaaaatattggtgttgtgattaaatgtttttaaattagttttttttaatactatctttctgatatattcttttcttttcctttgatgaag

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgta------tatttgttca-gtactgatgaatcctcattttcagctgtaaga--gttcagctttgatgtaaactgttggcctaatacatttgctgtttcag
|||| | ||||||||||| || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| || ||||| || |||||||||      | ||| || | |||   |  ||| || |||||      | |||  |||  |   |  | |       |    |||||   ||      |   
TGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTCTAATATACTCTAAGCAGgtagaggcttgtttatttatgtatcaaataatactgatttttgttcatcagattgttttgtgcttctcttgttaaattctttaatattgttatgacctat-

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtat-------atttgttcagta---------ctgatgaatcctcattttcagctgtaa---gagttcagctttgatgtaaactgttggcctaatacatttgctgtttcag-----------------------------------------
 ||  |||||||||  || || || || || || || ||||||||||| || |||||||| || ||||||||||||||||| || ||||| ||||||||||||        |||| || | ||          | ||  | |   |     ||  |||    |||||    |||| | | |     |   ||||| |||||  ||||| |                                          
CGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTCTGATATACTCAAAGCAGgtaatgaaacaatttttttattaggcttttattttatagaacaataaaaatagtggtactatgagttatattttggtctcattacataatctaat-cattttttgttttatagtagatgttaaatgtattttttcccttttatttgctgaag

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcat----------tttcagctgtaagagttcagctttgatgt-----aaactgttggcctaatacatttgctgtttcag-----------
|||  ||||||| || || || ||||| || || || ||||||||||| |||||||| || || ||||||||||| |||||||| |||||||| |||||||||| ||  || |||   |  ||||| | |           ||     |  | |  || |  |||| | |     | ||| |  | || || ||||   |  ||              
TGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCCTGATATATTCTAAGCAGgtattttgttttagtttagtagaatcataaaaatgctggtgttgtgattaaatgtttttaaatttgttttttttaatactatcagtctgatgcattcttttcttttcctttgatgaag

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 12
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattttc---agctgtaagagttcagc--tttgatgtaaactgttggcctaatacatttgctgtttcag---
|||  |||||||||  || || || || || || || |||||||| || || |||||||| || ||||||||||||||||| || ||||| ||||||||||||         | |  | || |  | | |||||    | |  ||| |    ||   | |||  || | | | | |  | |||||   ||  |       
TGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTGGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTCTGATATACTCAAAGCAGgtaatgaaacaaattttttattaggctttattttatagaaccataaaatagtagtaatatgagttatattttggtctcattacataatctaataattttt

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtata--tttgttca-gtactgatgaatcctcattttcagctgtaagagt--tcagctttgatgtaaactgttggcctaatacatttgctgttt-cag----------------------------------------------------------------------------------------------------
|||  | ||||||||||| || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| || ||||| || ||||||||| |   ||||| | |||   |  ||| || |||||      |  || |  |  |   |  | |       |    |||||   ||      |  ||                                                                                                    
TGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTCTGATATACTCTAAGCAGgtagaagcttgtttatgtatcaaataatactgatttttgttcatctgattcttttgtgcttctcttgttaaattctttaatattgttatgacctatagaggttttaattggcctgtataattaacattgcatatcttgcctttgcattttactggaacaaattgtggctgatcattttcattactttttccgctacag

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattttcagctgtaagagttcagctttgatgtaaactgttggcctaatacat-ttgctgtttcag-------------
|||||| ||||||||||| || ||||| || || || ||||| ||||| |||||||| ||  ||||||| |||||||| ||  | || ||||||||||||||| |    || |||  | |  | |   |    || | ||| |  ||| | | |  | || |  |||  ||  || |  |     ||||| |              
TGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATATTGATTTATTCAAAGCAGgtaaaca-attaagttttaa--agtttgccccctccgttgttat-gtttaccctaaaggtca-ttgt--gctcaagaggtaccattgttttatgttgtgactctag

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattt-tcagctgta----agagttcagctttgatgtaaactgttggcctaatacatttgctgtttcag
 ||||||||||||||||| || ||| |||| || || |||||||| || |||||||| ||||||||||| |||||||| || || || || ||||||||||||         |    |  |  | |||| | | | |  | ||    | ||||| | | |    | || |       |   | ||| |    |||||
CGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATACTGATTTACTCAAAGCAGgtaagcaataagatctatagtataacctcttctattatttttaccctaaagttctgttgtctcatgaattaccattgtttcatatt-gtgacttcag

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 13
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattttcagctgtaaga--gttcagctttgatgtaaactgttgg--cctaatacatttgctgtttcag-------------------------------------------------------------------------------------------------------
||| ||||||||||| || || |||||||| || || ||||||||||| || |||||||| || ||||| || || || || || ||||| || |||||||||||| | ||  ||| |  |  |    | |       | |||||   ||     |  |  |  | |  |    | || ||  || |   ||| |                                                                                                        
TGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTCTAATATACTCCAAGCAGgtatatatattttgtattctttcaattacctaaatctttttaagattattttctgtcaaaatctattactaaatcatagtagtttgggaattttatcatattatatagcacaatgcatatactatctatgcccttatcattattttttattgctattctttgaatggtctttgtacttctgattttttcatctatgcag

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: 73 (upstream exon), 60 (downstream exon)
Score: 81

TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgt ... gctgtttcagGTTGGATACACCCCTGACTACCTCTTCCTCCTCCAGACCATTTTACGTACGGATCCACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCCTTATATATTCAAAGCAGgtatatttgttcagtactgatgaatcctcattttcagctgtaagagttcagctttgatgtaaactgttggcctaatacatttgctgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG