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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttag

Basic information

species Oryza sativa
transcript LOC_Os05g11140.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaa------ctcttatttatgttag
 ||| ||||||||||||| ||||| ||||||||||||||||| |||||| ||||||||||||| || ||||||||             |||||    ||| | ||  | |   ||||| | ||||| ||  ||  | | |||  ||||||||      ||||| |||||| |||
TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtac------------ctgatgtagtctagtcaaaggatagtaata-tattttgtatactgtgtatagaatgatagctaaagaaatctcttgtttatgatag

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G01890.1 (Glycine max), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgca---tgttgcattt-tgaaatatagctaactcttattta-tgttag
 ||| |   ||||||||||||||||||||| || |||||||| || |||||||| || ||||| ||   |||||| || |  |     |   |  | ||    || ||||    |  |  | ||   |   | |||||||| |    | ||   |     |||||| | || |
CATGACCACTGAAATGGTTGCTTGTATTGCCATTGAAGCAATATCTATATTGGAAAAAATGCACTCTCGAGGgtaattttcataccacccactaatttcaataca-tgaattacataaactcttgataaagttttgcatttatttcctttaaacattgaatatttaatatttg

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattt-tgaaatatagctaactcttatttat--gttag--
 ||||||  |||||||||||| |||||||| || || || ||||||||||| |||||||||||||| | |||||  | | |  |||   ||||  | | |  |   |    |   ||  | ||||   ||    |||| | |  | |   |   || ||    |   ||||  
GATGTCTACTGAAATGGTTGCATGTATTGCAATTGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGGgtgat-gctcattttcttgattatgtttatgatttatttctggattttattttctttgacagatttgttagttctgaatgcttcctaaccgttgattagaa

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G09070.1 (Glycine max), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcatt--ttgaaatatagctaactctt--atttatgttag-
 ||||||  |||||||||||| |||||||| || || || ||||||||||| |||||||||||||| | |||||  | |    |||  |||||  | | |  |   |    |   ||  | |||| | ||    |||  ||  | |  ||    ||     | | ||    | 
GATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGGgtgat-gcccattttcctgattatgtttatgatttatttctggattttattttccttgacagattggttacagttcagaatgcttcccgactaataaccgt

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G21570.1 (Glycine max), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttg--------gcagtgaagcctaatagttttttgcatgttgcattttgaaatatagc-taactcttatttatgttag
 ||| |    |||||||||||||||||||| || |||||||| || |||||||| || ||||| ||   |||||| || |  |     |   |  | || |          ||   |  | | |||  ||||||||| |      || | | || |   |  || |||||       
CATGACCACCGAAATGGTTGCTTGTATTGCCATTGAAGCAATATCTATATTGGAAAAAATGCACTCTCGAGGgtaattttcataccacccactaatttcatacatgaattacataaactcttgataaatttttgcatttatttcctttagacattgaacatttcatatttgc-----

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcatt--ttgaaatatagctaact--cttatttatgttag-
 ||||||  |||||||||||| |||||||| || || || ||||||||||| |||||||||||||| | |||||  | |    |||  |||||  |   |  |   |    |   ||  | ||||   ||    |||  ||  | |  ||    ||  || | | ||    | 
GATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGGgtgat-gcccattttcctgattatgcttatgatttatttctggattttattttctttgacagattggttacagttcagaatgcttcctaactaataactgt

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtt-----tttttctctgatcc----tctcttggcagtgaagcctaatagttttttgcatg--ttgcattttgaaatatagctaactcttatttatgttag
 |||||  |||||||||| || ||||||||||| ||||||||||| ||||| ||||||||||| || | |||||   |  |     | |   | |||| |    | ||||     | | |   || | ||| |  || |  ||| |  |  | |    | |     | ||||||     
GATGTCCATTGAAATGGTAGCATGTATTGCTATTGAAGCAATCTCTATATTAGAGAAGATGCACTCTAGAGGgtgagtactattaatctgcttatgatgcctgttttctttagtataaggaaaaagattttgtaccagggtttggacctctaga---gggtggacatgatttatc----

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 6
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttag-------
 |||||  ||||||||||||| || |||||||| |||||||| |||||||||||||||||||| || | ||||||    |||| | |    | || |         ||   |||  | |||||||   | || | ||||    |   | |   | ||| | || | |        
TATGTCCATTGAAATGGTTGCATGCATTGCTATTGAAGCAATATCCATATTGGAGAAGATGCACTCCAGAGGgtaagaattttctgccacaaaccaca---aattttgtttccttcttgtttttttttttttccttttttcttttgcgttttattttaataatatgaaggatctt

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|29681938|gb|CB678213.1|CB678213
EST:     TGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG                         GTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGG
genomic: TGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgttt ... tttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttag

- - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG