Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcataaatcttgtgaaagacttttggtatatgctttcaaaagtaatgacagtgccatagtatctaggtgcttgttgtcaaggtgctagattacc...

Basic information

species Oryza sativa
transcript LOC_Os06g05180.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 18
GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcataaatcttgtgaaagacttttggtatatgctttcaaaagtaatgacagtgccatagtatctaggtgcttgttgtcaaggtgctagattacc-------
|||||||  || ||||| || ||||||||||| |||||||||||||||||||| || |||||||||||||||||| |||  | || |||  | |||    || |||| ||   |  ||| |||  ||| |||  ||| |  || ||  |||  |      | |    |   |       
GCTATCGTCATAGAAGCACAGAGTGAATCTAAATGGAAGCAGTTGGGTGAACTCGCCATGTCCACAGGCAAGgttggtttgtgaaccttacggaag----tttgtatttggcatttaaa-taactacattgc--taggaaataagtttttgaggatggaataccttttctacagtgtga

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 4
GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcataaatcttgtgaaagacttttggtatatgctttcaaaagta-atgacagtgccatagtatctaggtgcttgttgtcaaggtgctagattacc--
|||||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||||||||||||| || |||  ||| | |      | |  |  |   ||  | ||||| || ||   |  | |   | | |  | | |    |   |||     |  |   
GCTATCGCCATAGAAGCACAAAGTGAATCTAAATGGAAGCAGTTGGGCGAACTTGCCATGTCCACAGGCAAGgttagctcttaagccttatca---gtctgtatttgacatttaaataagtacattactaagaaacaaatttttgaggatggaatacctcgtgtagtgtggcgtt

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 8
GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcataaatcttgtgaaagacttttggtatatgctttcaaaagtaatgacagtgccatagtatctaggtgcttgttgtcaaggtgctagattacc--------
|||||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||||||||||||| || |||  ||| | |       |  |||| ||   |  ||| ||   ||| ||| | || | | || |  |     |  |    || |  ||          
GCTATCGCCATAGAAGCACAAAGTGAATCTAAATGGAAGCAGTTGGGCGAACTTGCCATGTCCACAGGCAAGgttagctcttaagccttatcag------tctgtatttgacatttaaa-tatgtacattgcta-agaaacaagtttttgaggatggaatacctcgtgtagtgtggcgtt

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 19
GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcataaatcttgtgaaagacttttggtatatgctttcaaaagtaatgacagtgccatagtatctaggtgcttgttgtcaaggtgctagattacc--------
|||||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||||||||||||| || |||  ||| | |       |  |||| ||   |  ||| |||  ||| ||| | || | | || |  |     |  |    || | |||          
GCTATCGCCATAGAAGCACAAAGTGAATCTAAATGGAAGCAGTTGGGCGAACTTGCCATGTCCACAGGCAAGgttagctcttaagccttatcag------tctgtatttgacatttaaa-taagcacattgcta-agaaacaagtttttgaggatggaatacctcgtttagtgtggcgtt

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|2443004|gb|C74775.1|C74775
EST:     GTGAATCTAAGTGGAAGCAGTTNGGTGAACTGGCTATGTCCACAGGCAAG                         CTAGATATGGCGGAN-AGTGCCTTGTGCAAGCGAAGGACTTAA
genomic: GTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcat ... acttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcataaatcttgtgaaagacttttggtatatgctttcaaaagtaatgacagtgccatagtatctaggtgcttgttgtcaaggtgctagattacc

- - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - -  TGGAAG