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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagttttcccaggggtaatatgaaactctttttcattttaccttttgagtgttccatattagctactgatgcaaatcctggctgccatgttaactttgcacctttgaattcaactattgtgttctctttccatattctgacatatcatactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTAAATGTACTAATCGAAAAAGAAAACCAGGATGGACAATGGGCATATGGTA

Basic information

species Oryza sativa
transcript LOC_Os05g39230.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g39230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AC197705.4_FGT011 (Zea mays), 3'ss of exon 7
gtaaaagttttcccaggggtaatatgaaactctttttcattttaccttttgag-tgttccatattagctactgatgcaaatcctggctgccatgt-taactttgcacctttgaattcaactattgtgttctct----ttccatattctgaca------tatcatactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTAAATGTACTAATCGAAAAAGAAAACCAGGATGGACAATGGGCATATGGTA
                |   || |  |  |  |   |  | |    || |||| ||   |  ||  | | ||||| ||| || |   |   |||  ||  |||||||| |  ||||    |||| |||| | |     ||  | |  |||||       ||||| || ||||||||||||||||| |||||||| |||||||| || ||||||||||| || ||||| || || || ||| |||| |  || || | |||| ||||||| |
----------------gtaaaacaaaaggcattaagtactatcctattctgaggtggctcccatgtgttgctgatacaagtcatta-tataatgcctatttttgcaccatcaaattgg--tattctgttgtttgaaactctttgtgttgacaacttgacatcatgcttcagAAATTAGGTTTTGCATCTTGTGAGCGAAGACCTGGGGCTACTGAAGGAGTGAATGTCCTTATTGAGAAACAAAATCTTGAGGGGCTATGGTCATATGGCA
















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|29689746|gb|CB686021.1|CB686021
EST:     CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG                         AAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA
genomic: CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA
EST: gi|58602199|gb|CK012727.1|CK012727
EST:     CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG                         AAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGG
genomic: CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGG
EST: gi|8856717|gb|AU094035.1|AU094035
EST:     CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG                         AAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA
genomic: CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgaattcaactattgtgttctctttccatattctgacatatcatactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTAAATGTACTAATCGAAAAAGAAAACCAGGATGGACAATGGGCATATGGTA
                                  ttctgac  putative branch site (score: 2)
                                         atatcata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagttttcccaggggtaatatgaaactctttttcattttaccttttgagtgttccatattagctactgatgcaaatcctggctgccatgttaactttgcacctttgaattcaactattgtgttctctttccatattctgacatatcatactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTAAATGTACTAATCGAAAAAGAAAACCAGGATGGACAATGGGCATATGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA