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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgtttactgtccttttctttacgctatcttctctgctcttatattattctttatttaccag

Basic information

species Oryza sativa
transcript LOC_Os02g44642.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AC209208.3_FGT001 (Zea mays), 5'ss of exon 3
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgttt--actgtccttttctttacgctatcttctctgctcttatattattcttta-tttaccag------------------------------------------------------------------------------------
||| | ||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | || ||||||||   | ||  | || ||||  ||  |  |      || ||    ||   | ||    ||  |  |   |  || ||                                                                                      
TGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAGgtatggtgtcttg-tacatgtttgcacaatattgaaaactaggcctgtttggtttcttgcctaagacaccacaacttgcctaagctagtgactaagcttagacaagttgtgaccatcatgcctcatgctgtactttctcttttaacattattatttcatttcacag

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G093316_T01 (Zea mays), 5'ss of exon 4
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttt-----tctccacgtttactgtccttttctttacgctatcttctctgctcttatatta-ttctttatttaccag------------------
||| ||||||||||||||||| ||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||| |||| ||||||||   ||||     | | |||  | | | |      ||  ||    || ||    ||| |    || ||| |  |||| ||                   
TGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAGgtatgttgttttgtacatgttcacactcaatattgaaaactacacatgttcatcatgcctcatgctgtacttcctcttttaacattattatcacatctcacag

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G30030.2 (Glycine max), 5'ss of exon 4
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtat---gacatttttctccacgtttactgtccttttctt--------tacgctatcttctctgctcttatattattctttatttaccag-----------------------------------------------------
 || |  |||||||||||||| ||||| ||||| || ||||| ||||| ||| | ||||| ||||| ||||| ||||| ||    ||||||    ||  |  || |  || |||    |  |||| |         ||   |  ||| |   |  || |   ||   | | |  | |                                                      
GGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAGgtaaatagatttcctttttgacctttgaaatttttttgtgggactgaatagatttcctttttgacctttgtgcaatatgtcagtatctatttctgtttcaaatttggtgtagctttgaaaatctaactcccagattctggcag

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G24970.2 (Glycine max), 5'ss of exon 3
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgta---tgacatttttctccacgtttactgtccttttct---ttacgctatcttctctgctcttatattattctt-tatttaccag-------------------------------------------------
 || |  |||||||||||||| ||||| ||||| || || || ||||| ||| | ||||| ||||||||||| ||||| ||    ||||||   |||  |  || |  || |||    |  |||       |     ||| ||  |  |  |  |  || ||  ||| ||                                                     
GGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAGgtaaattgatttcctttttgacctttgaaattttttgtggggctgaataatcctcattctttgtgcaaaatgctagtatctatttctgtttcaaatttagtgtagctttcaaatctaactcctagattctggcag

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G42960.1 (Glycine max), 5'ss of exon 3
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgtttactgtccttttctttacgctatcttctctgctcttatattatt------ctttatttaccag------------------
||| |  ||||| |||||||||||||||||||| || ||||| ||||| ||| |||||||||  ||||||||  | ||  |  | || ||| |   ||  |||   || |||     |||  ||  |    || | |     | ||| | |         ||| ||||||                     
TGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAAgtaag--cttgctcttatcgattaacacacttc-ctccattacatatgcctcatttttaaagtggaaaacaacttaatttactgaattaccattaccccctcc

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G01880.1 (Glycine max), 5'ss of exon 3
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgtttactg---tccttttctttacgctatcttctctgctcttatattattctttatttaccag--------------------
 ||    ||||| |||||||||||||||||||| |||||||| || || ||| |||||||||  ||||||||  ||||  |  | || ||| | | |  || |  |  ||   ||   | | ||||| |   | || ||   || | ||| | |    ||| |||   |                     
AGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAAgtaag-cttgcttgtgtagattaggtggaatacatttctatgatccattttacttgtt-ttacacttgcttttctttgggaatgtccatattatgtctcatt

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G24970.1 (Glycine max), 5'ss of exon 4
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgta---tgacatttttctccacgtttactgtccttttct---ttacgctatcttctctgctcttatattattctt-tatttaccag-------------------
 || |  |||||||||||||| ||||| ||||| || || || ||||| ||| | ||||| ||||||||||| ||||| ||    ||||||   |||  |  || |  || |||    |  |||       |     ||| ||  |  |  |  |  || ||  ||| ||                       
GGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAGgtaaattgatttcctttttgacctttgaaattttttgtggggctgaataatcctcattctttgtgcaaaatgctagtatctatttctgtttcaaatttagtgtag

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G02520.1 (Glycine max), 5'ss of exon 6
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctcca-cgtttactgtccttttctttacgctatcttctctgctcttatattattctttatttaccag-------------------------
||| |  ||||| |||||||||||||||||||| || ||||| ||||| ||| |||||||||  ||||||||  | ||  |  | || ||| |     || ||| | || |||     |  ||   ||  |  || | | |    |   |     | | |||||||                           
TGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAAgtaag----cttgctctatcgattaacacaccattacatatacc-tcatttttaaagtggaaaacaacctaatttacccccccccccccccccctcctttactaa

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 5'ss of exon 3
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacattt---ttctccacgtttactg----tccttttctttacgctatcttctctgctcttatattattctttatttaccag---------------------------------------------------------------------------------------------
||| |  |||||||||||||||||||||||||| || || || ||||| ||| | || ||||| ||||||||||| |||||| | || ||| |   |||   |||  ||   |||| |    ||| ||||   |    ||    | || |  | |  ||  | || | |                                                                                                  
TGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAAgtaagttgtttccattcagcagaattacagaggttccatttcacaaaaggatgcagtttgttgcttttctacacattttctgttgtttgtcttttcaaatgagaatctctctccatttacttcctgttttggtgttttacatagtttgagggaagttcttactctcagtgctttggcag

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ36728 (Selaginella moellendorffii), 5'ss of exon 1
------------TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgtttactgtccttttctttacgctatcttctctgctcttatattattctttatttaccag
              ||   ||    |||||||| |||||||| ||  | ||||| ||||||||| | || ||||||||||||| ||||||| |  |||||||| || |    | |  | | ||   |      |    | || ||| | |||   | |  |                  
TTGTTTCAGTGAGAATGTCGGCCGCATGTGTGCCATGAAGGAAGTTCCGCTTTTATCAGACGATTCCAAGTCAAAAGAAAGTGTAAAGCAGCTAAGTCAGgtacga-agaactttgaatgcttcaagc-----ttacaaggcgatcatttctaaaccttcag-----------------

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ27940 (Selaginella moellendorffii), 5'ss of exon 1
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgtttactgtccttttctttacgctatcttctctgctcttatattattctttatttaccag
             |||||||| |||||||| ||  | ||||| ||||||||| | || ||||||||||||| ||||||| |  |||||||| || |    | |  | | ||   |      |    | || ||| |  ||   | |  |                  
-------------ATGTGTGCCATGAAGGAAGTTCCGCTTTTATCAGACGATTCCAAGTCAAAAGAAAGTGTAAAGCAGCTAAGTCAGgtacga-agaactttgaatgcttcaagc-----ttacaaggcgatcattcctaaaccttcag-----------------

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: 52 (upstream exon), 73 (downstream exon)
Score: 7

TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatt ... tatttaccagGAAATATTACTTCTGAATCGTCTGCAACATCCAAATATTGTACGATACTATGGATCTGAAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAGgtatgacatttttctccacgtttactgtccttttctttacgctatcttctctgctcttatattattctttatttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG