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

GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttctctatctgcgatattgctaaccatcttcttctctccaaattcgagatttgttcacattgttatatatactcag

Basic information

species Arabidopsis thaliana
transcript AT5G66120.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 5'ss of exon 6
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgta------tctttctctatctgcgatattgcta----accatcttct-tctctccaa-attcgagatttgttcacattgttatatatactcag------
|| |||||||| ||   |||||||||||  ||||||||||| || |||||||||||||| || |||       ||   | | | | | | |   | |    |  || || | ||  | ||  | |     |||| |    ||  ||| |   | |        
GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTTGCAGCTGGAACAgtaagaacacctgaatatttttacaacacctcgatttcattattttgtatcgtttcattacttatcttttggttctgtttctatgttgccaccactctag

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 6
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttctctat-ctgcgatattgctaaccatcttcttctct----------ccaaattcga--gatttgttcacattgttatatatactcag--------
|| |||||||||||  |||| |||||  ||||||| |||||||| |||||||||||||||||||||| |||    |  |    ||||    ||   |  |  | | |          | ||| || |  | | | ||   ||   | | ||| |  |         
GCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtattttttaaaaaacaaaaatatcatgaattgtacttatatttgtgtttaatactaaagtctataggtctattttgatgaatctgtatgccaatgtacacag

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G08350.1 (Glycine max), 5'ss of exon 6
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttctctatc-tgcgatattgctaaccatcttcttctct----------ccaaattcga--gatttgttcacattgttatatatactcag--------
|| |||||||||||  | || |||||  ||||||| |||||||| |||||||||||||||||||||| ||| | ||       |||| |  ||   |  |    | |          | ||| || |  | | | ||  |||   | | ||| |  |         
GCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtatttttttttaaaacaaaatatcgtgaattgtacttacatttgtgtttaatactaaagtctataggtctattttcatgaatctgtatgccaatgtacacag

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G08350.2 (Glycine max), 5'ss of exon 6
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttctctatc-tgcgatattgctaaccatcttcttctct----------ccaaattcg--agatttgttcacattgttatatatactcag--------
       |||||||  | || |||||  ||||||| |||||||| |||||||||||||||||||||| ||| | ||       |||| |  ||   |  |    | |          | ||| ||   || | | ||  |||   | | ||| |  |         
-------AAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACGgtatttttttttaaaacaaaatatcgtgaattgtacttacatttgtgtttaatactaaagtctataggtctattttcatgaatctgtatgccaatgtacacag

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 6
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtat--ctttctctatctgcgatattgctaa-ccatcttcttctctcca---aattcgagatttgttcacatt--gttatatatactcag-------------------------------------------------------------------
|| |||||||||||  ||||||||||  ||||||||||||||||||||||||||||||||| |||||    | | | || | |  | || || | ||| || |   | | ||   || ||   ||   | | |||      || ||| ||||                                                                    
GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATGgtatggtatccacaattttctgttttcctcatccacctccccttgttcagtcaagtctgtatacatccgcatgcaagcatgtatgctcatgggtgtatttgtgtgtccttatctctttttttgatcactatcatgtgtattctgcaccaatgtttag

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|116450338|gb|EG492930.1|EG492930
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG                         GTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
EST: gi|116421960|gb|EG464552.1|EG464552
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG                         GTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
EST: gi|116421951|gb|EG464543.1|EG464543
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG                         GTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
EST: gi|125323959|gb|EL338039.1|EL338039
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGTAGCTGGCACG                         GTAATGGCAGTGG
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGG
EST: gi|116421921|gb|EG464513.1|EG464513
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG                         GTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
EST: gi|116472854|gb|EG515446.1|EG515446
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG                         GTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
EST: gi|116421964|gb|EG464556.1|EG464556
EST:     GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG                         GTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT
genomic: GCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttct ... atatactcagGTAATGGCAGTGGACATGTCATATCGTCTTGGTTGGATCGATGAATCGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACGgtatctttctctatctgcgatattgctaaccatcttcttctctccaaattcgagatttgttcacattgttatatatactcag

- - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG