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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcagcctgagcacacatacccctgctgtatgctgctttaatctgtttcagtttcttattgcactatgtttccactatttttcag

Basic information

species Oryza sativa
transcript LOC_Os06g02380.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag--cctgagcacacatacccctgctgtatgctgctttaatctgtttcagtttcttattgcactatgtttccactatttttcag-----------------------------------------------------------------------------------------
|||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||||||| ||||||| || ||||||||||||||| ||  |     ||||    ||   |  |  | | ||||| |||| |   || | |||||  |    |  |      |     | ||  |                                                                                         
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctg-tttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgta--gcttcagcctgagcacacatacccctgctgtatgctgctttaatctgtttcagtttcttattgca-ctatgtttccactatttttcag
||| |||||||| ||||| ||||| ||||| ||||||||||| || || || ||||| |||||||| ||||||||| | |  |||||||||||||| |||||    | |  | |||    | |     | ||   |||  |  |||||  |  |||| | | | |||  | || |   |    | || | |||
TCTATATGTTGTCGAGGGGATGCAATTTGACCGTGGTTATATTTCTCCATACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatttgtctgttttccctgtaacttgt--tattattttttaacatccttca-tatttaattataactttacatggtatgttatgcag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcagcctgagcacacatacccc-tgctgtatgctgctttaa--tctgtttcagtttcttattgcactatgtttccactatttttcag
||| |||||||| ||||| ||||| || || ||||||||||| || || || || || |||||||| ||||||||| |||  || ||||||||||| |||||        | |  |      | |||   |   |||  |  |||||  ||   |  | || ||||| ||  ||| |      | || | |||
TCTGTATGTTGTTGAGGGGATGCAATTCGACCGTGGTTATATTTCTCCATACTTCGTTACTGACAGTGAGAAAATGGCTGTTGAGTATGAGAACTGTAAGgtga----gacatttgtctgttttccctgcgaattattattttttaacatcctgtgtatttacttatagctttatatggta--tgttatgcag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtag------cttcagcctgagcacacatacccctgctgtatgctgctt--taatctgtttcagtttcttattgcactatgtttccactatttttcag------------------
 ||||| || || || |||||||| ||||| |||||||||||||| || || ||||| || ||||||||||||||||| |  || |  || || ||||||||||      ||| |  ||||| | | | |    |  |||  || |  |  | | |   |  || |  ||||       | |  | || || ||| |                   
CCTCTACGTCGTAGAAGGAATGCAATTTGACCGTGGTTATATCTCTCCTTACTTTGTGACAGACAGCGAGAAAATGTCCGTCGAGTTCGACAATTGCAAGgtagatgtttcttgaatctgagtaga-agatgaattttgttggcagactatttagccactaaagatatttatatatgagtataacaacgatctttaatgttttggtatgattgcag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G56500.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcagcctgagcacacatacccctgctgtatgctgctttaatctgtttcagtttcttattgcactatgtttccactatttttcag--
 || || ||||| || |||||||| ||||| |||||||||||||| || || ||||| || ||||| |||||||||| |||||||||||||||||||||||||   | |   |    |||  ||   ||  |    |||| |  ||       |||| | || |  |  ||||| ||  ||   |||     
CCTTTACGTTGTTGAAGGAATGCAATTTGATCGTGGTTATATCTCTCCTTACTTTGTCACCGACAGTGAGAAAATGTGTGCAGAATATGAGAACTGCAAGgtattattattgtttatacagttaaatct--taatagctgat--aaaaaaccgcagtattttttgactatatgtctcttcttgcttttgtag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcagcctgagcacacatacccctgctgtatgctgctttaatctgttt--cagtttcttattgcactatgtttccactatttttcag
 || ||||||||||| |||||||| ||||| ||||||||||||||||| || ||||| || ||||| |||||||||||||  || ||||| || |||||||||  ||     |   |  |  ||||       |||  || |  ||   |  |  ||  ||  || ||  |                     
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttctttattctgagctaccaaaatgatattgtgatgcaaatagcctaacaagtttctactgtgcag-------------------

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgta----gcttcagcctgagcacacatacccctgctgtatgctgctttaatctgtttca----gtttcttattgc--actatgtttccactatttttcag---------------------------------------
  | ||||||||||| |||||||||||||| |||||||||||||| || || || || || ||||| ||||||||| |||  |||||||| || |||||||||    ||     | | ||||    |   ||   |     |      ||| ||   |     ||| ||| || |  ||| || ||  |      |||                                         
CTTGTATGTTGTGGAAGGAATGCAGTTTGATCGTGGTTATATCTCTCCTTACTTCGTCACAGACAGTGAGAAAATGGCTGTTGAATATGAAAATTGCAAGgtaagaggccaagacttcagcattttttttccatatagtctccaaggaaatatgaccctaagtgttacttgttactgactctggttttatctcccttcgttttattatattgatttttttgggacatctgtttatgcag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgta-gcttcagcctgagcacacat-acccctgctgta-tgctgctttaatctgtttcagtttcttattgcactatgtttccactatttttcag----
 || |||||||| || |||||||| ||||| |||||||||||||| || || ||||| || || || ||||||||| | |  ||||  ||||||||||||||  || |    || |  |   |  |   ||  | |  | || ||  ||  || |||  |||||   |   |||  |  | | | || ||||     
CCTGTATGTTGTTGAAGGAATGCAATTTGACCGTGGTTATATCTCACCTTACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttc--tttctggct-ttctaactgacaaattttgttcatgtag

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|7212769|gb|D47177.2|D47177
EST:     ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAG                         CTTCTTTTGGTGGACNNNNNNNTCACCAACGCAAGGGATCTTATCAATGTT
genomic: ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag ... tatttttcagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTT
EST: gi|7212768|gb|D46006.2|D46006
EST:     ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAN                         CTTCTTTTGGTGGACNNNNNNNTCACCAACGCAAGGGATCTTATCAATGTT
genomic: ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag ... tatttttcagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTT
EST: gi|88325601|gb|CI648035.1|CI648035
EST:     ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAG                         CTTCTTTTGGTGGACNNNNNNNTCACCAACGCAAGGGATCTTATCAATGTT
genomic: ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag ... tatttttcagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTT
EST: gi|86906130|gb|CI292661.1|CI292661
EST:     ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAG                         CTTCTTTTGGTGGACNNNNNNNTCACCAACGCAAGGGATCTTATCAATGTT
genomic: ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag ... tatttttcagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTT
EST: gi|33797089|gb|CF324410.1|CF324410
EST:     ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAG                         CTTCTTTTGGTGGACNNNNNNNTCACCAACGCAAGGGATCTTATCAATGTT
genomic: ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag ... tatttttcagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTT
EST: gi|58690567|gb|CK079254.1|CK079254
EST:     ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAG                         CTTCTTTTGGTGGACNNNNNNNTCACCAACGCAAGGGATCTTATCAATGTT
genomic: ATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag ... tatttttcagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcagcctgagcacacatacccctgctgtatgctgctttaatctgtttcagtttcttattgcactatgtttccactatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG