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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCATCTGTTCATGGAGATAAGTTAAGACACGAGCTTGCTAGAGACCTTACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagtttatgataatatattcgtttttgctacctgctatgtcaatatttgctaatgcattggtgtgctacttgtgatcttatatatttttgcatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G07100.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G07100.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os04g04020.1 (Oryza sativa), 5'ss of exon 8
CAATCATCTGTTCATGGAGATAAGTTAAGACACGAGCTTGCTAGAGACCTTACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagtttatgataatatattcgtttttgctacctgctatgtcaatatttgctaatgcattggtgtgctacttgtgatcttatatatttttgcatgcag
||  ||  |  |||||| |||||  | | ||| ||||||   |||||||||||| |||||||||| |||||  | |||||||| || ||||||||||||||||    || | |  ||| | ||   |||||   || | |||        | |  || |   | || ||| || ||||                         
CAGGCAGTTACTCATGGGGATAAACTCAAACATGAGCTTAGCAGAGACCTTACACGGGAAACTGCATGGGAATCTGTTATGCGTATCAGATGTGGAAAAGgttctg-agctgacaatattttaaa-gttttatttatcagcttaacattcaatgacttacaaactgatgt-ctgcttgcag----------------------

upper sequence: AT3G07100.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv19s0014g01900.t01 (Vitis vinifera), 5'ss of exon 8
CAATCATCTGTTCATGGAGATAAGTTAAGACACGAGCTTGCTAGAGACCTTACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagtttatgataat--------atattcgtttttg---ctacctgctatgtcaatatttgctaatgcattggtgtgctacttgt----gatcttatatatt----tttgcatgcag-----------------------------
  ||||    ||||   ||||| ||| ||||| |||||  | || |||||||||||||||||||| ||||| || || ||||| ||||||||||| ||||||  ||  |||  ||| | |        ||     || |||    ||  |  |   |   | ||| ||  |  |||    |  ||||| |    |||||| |  |||    ||||  | | |                             
TTATCAATCATTCACAAAGATAGGTTGAGACATGAGCTATCCAGGGACCTTACAAGGGAAACTGCCTGGGAAGCTGTCATGCGCATAAGATGTGGCAAAGgtccaactgttcctgaaactcttcaaccatcacaattcttgagattattttttcccttttttttttcttgtaaattttaattttacttcttcaagatcttgttaattgctatttgggtactgaaagttgaatctttttcctgtaattttag
















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|116442285|gb|EG484877.1|EG484877
EST:     TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAG                         GAATTCGTTTCTCGTCCTACCATGGGAACTTCATGCTAAGGTCTACTGACC
genomic: TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagt ... ttgcatgcagGAATTCGTTTCTCGTCCTACCATGGGAACTTCATGCTAAGGTCTACTGACC
EST: gi|125042815|gb|EL115084.1|EL115084
EST:     TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAG                         GAATTCGTTTCTCGTCCTACCATGGGAACTTCATGCTAAGGTCTACTGACC
genomic: TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagt ... ttgcatgcagGAATTCGTTTCTCGTCCTACCATGGGAACTTCATGCTAAGGTCTACTGACC
EST: gi|86068051|gb|DR363808.1|DR363808
EST:     TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAG                         GAATTCGTTTCTCGTCCTACCATGGGAACTTTCATGCTAA
genomic: TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagt ... ttgcatgcagGAATTCGTTTCTCGTCCTACCATGGGAACTT-CATGCTAA
EST: gi|164009806|gb|ES109028.1|ES109028
EST:     TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAG                         GAATTCGTTTCTCGTC
genomic: TACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagt ... ttgcatgcagGAATTCGTTTCTCGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCATCTGTTCATGGAGATAAGTTAAGACACGAGCTTGCTAGAGACCTTACAAGGGAAACTGCGTGGGAGGCGGTTATGCGAATAAGATGTGGAAAAGgtttaatagtttatgataatatattcgtttttgctacctgctatgtcaatatttgctaatgcattggtgtgctacttgtgatcttatatatttttgcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG