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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCTAAAAAGCAAGTTCTGGGGTCGCTCCATTCAACTTGATCCTGTTGGTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattacatatttagcaagaagtggttagatctttggtctgtggaaataattcacttgaaatattctatctcag

Basic information

species Oryza sativa
transcript LOC_Os03g49770.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G157172_T01 (Zea mays), 5'ss of exon 7
CAACCTAAAAAGCAAGTTCTGGGGTCGCTCCATTCAACTTGATCCTGTTGGTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattacatatttagcaagaagtggttagat-ctttggtctgtggaaataattcacttgaaatattctatctcag-----------------------
|||||| || || || ||||||||||| |||||||||||||||||||||||||   ||||  ||||||| |||||||||||||||||||| |||||||||||||  || ||||  |  |    |      | || | |   |||  ||| |||  ||  |  |  | |    | | |                        
CAACCTGAAGAGTAAATTCTGGGGTCGTTCCATTCAACTTGATCCTGTTGGTGCATTAACACTGGAGTTTGATGATGGTGAAGTTTTCCAATGGAGCAAGgtactcttgcataccttcctcagatcacaaatatacgtccatcta-ggatatacgtccatctaggtttgtcctataaattataagaaatatacattgacac

upper sequence: LOC_Os03g49770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G147332_T01 (Zea mays), 5'ss of exon 6
CAACCTAAAAAGCAAGTTCTGGGGTCGCTCCATTCAACTTGATCCTGTTGGTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattacatatttagcaaga----agtggttagatcttt--ggtctgtggaaat---aattcacttgaaatattctatctcag--------------
||||||||| || || ||||||||||| ||||| |||||||||||||||||||   ||||  ||||||| |||||||| ||||||||||| ||||||||||||| |||||||| ||     ||    |    ||||  | |   ||| |||   ||    || |   || |||  ||   |  |||              
CAACCTAAAGAGTAAATTCTGGGGTCGTTCCATCCAACTTGATCCTGTTGGTGAATTAACACTGGAGTTTGATGATGGGGAAGTTTTCCAATGGAGCAAGgtactattacatacttcctctgatcgcaaatattagcccatctaggtttgttctaagtcaaactttttttaaactttgactaccagtatagttttttata

upper sequence: LOC_Os03g49770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 5'ss of exon 6
CAACCTAAAAAGCAAGTTCTGGGGTCGCTCCATTCAACTTGATCCTGTTGGTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattacatatttagcaagaagtggttagatctttggtctgtggaaataattcacttgaaatattctatctcag-------------------------
|||  | ||||||||||| |||||||| || || ||||| |||||||| ||| | || || ||| | || ||||| |||||||| || || |||| ||||||||  |  | | |||  |||        |  |||||   | | |           || | |||  |   || |                            
CAATTTGAAAAGCAAGTTTTGGGGTCGTTCAATCCAACTGGATCCTGTCGGTATTCTCACGTTGAAATTTGATGACGGTGAAGTATTTCAATGGACCAAGgtacgct--cttgtttctcaattttgacatgaatcttaactttatcagtcctgaatacgtaaaagttcaaatgtggatgacccacgattcttgtgcctacta

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|29682317|gb|CB678592.1|CB678592
EST:     GTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAG                         GTGACAACTTCCATTTACAATCTCATATTGGGTAAACTGTATTGTGATCAT
genomic: GTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattac ... tctatctcagGTGACAACTTCCATTTACAATCTCATATTGGGTAAACTGTATTGTGATCAT
EST: gi|27546683|gb|CA764876.2|CA764876
EST:     TGTGCTAACCTTGGAGTTCGATGATGGGTGAAGTTTTNCAGTGGAGCAAG                         GTGACAACTTCCATTTACAATCTCATATTGGGTAAACTGTATTGNGATCAT
genomic: TGTGCTAACCTTGGAGTTCGATGATGG-TGAAGTTTTCCAGTGGAGCAAGgtaccattac ... tctatctcagGTGACAACTTCCATTTACAATCTCATATTGGGTAAACTGTATTGTGATCAT
EST: gi|163927376|gb|EG709904.1|EG709904
EST:     GTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAG                         GTGACAACTTCCATTTACAATCTCATATTGGGTAAACTGTATTGTGATCAT
genomic: GTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattac ... tctatctcagGTGACAACTTCCATTTACAATCTCATATTGGGTAAACTGTATTGTGATCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCTAAAAAGCAAGTTCTGGGGTCGCTCCATTCAACTTGATCCTGTTGGTGTGCTAACCTTGGAGTTCGATGATGGTGAAGTTTTCCAGTGGAGCAAGgtaccattacatatttagcaagaagtggttagatctttggtctgtggaaataattcacttgaaatattctatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG