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

GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag

Basic information

species Arabidopsis thaliana
transcript AT1G79920.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag
||| || || | ||| |||||||| || ||||| || ||||||||||| || ||   ||||||||| || ||||||||||||||||| ||||||||||| ||  ||    |  ||| |    ||||  || |   ||   ||  || ||      | |   | |  | |  |||  | |||||||
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttga----tcgattccactctttc-ctgacttcatctttagttagag------gcagaaactgataatatgttat-ttttcag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag
 ||||| || | ||| |||||||| || |||||||| |||||||| ||||||||    ||||||||||| ||| ||||||||||||| ||||| ||||| ||  |    |    |||  | || | ||           |||| | ||  |||||  | |   |  ||| || |||||  |||||
TGAGAATGAGTATGAAATGGCTCTTCAGGACAGAGTAATGGAAGAAACCAAGGAGAAAAAGAATGCTGTCGAGGCTTATGTTTATGACATGCGTAACAAGgtatg----ccgagtttaattttgtgatg----------atatatgaacatttgaacagtacctgatga-gtttcttgcgttcag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag
 ||||| || | |||||||||||| ||||||||||| |||||||| || |||||   |||||||||||||||  ||||||| ||||| ||||| ||||| ||          ||||  |||       |   | | |     | | ||||| ||||  |    |  ||   | |||| | || ||
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgta---------tattgagtcacgca--tactaatgttgtcttatgaagttgtgagcct--gattttgt--tctcttctatttag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G361605_T02 (Zea mays), 5'ss of exon 8
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgag-aaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag
 ||||| || | ||||||||||||||| |||||||| |||||||||||||| ||   ||| |||||||| ||  ||||||| ||||| ||||| ||||| ||  |   |  |  ||  | |  |    ||    ||   |||| | |   | |     | ||  |  |    |  ||||| || ||
AGAGAAAGAGTATGAGATGGCTCTGCAGGACAGAGTAATGGAAGAGACCAAAGAAAAGAAAAATGCTGTGGAAGCTTATGTCTATGACATGCGTAACAAGgtatgtggagatgcatgccctgatggtttttcttgtgaacataagcagtatct-----aatggtttttc---ttccttgtatttag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag
 ||||| || | |||||||||||| || |||||||| |||||||| ||||| ||   ||| |||||||| ||  ||||||| ||||| ||||| ||||| ||  |              |   | | |||   || | | | ||| |  |    |||||  | |       | | |||| || ||
AGAGAAAGAGTATGAGATGGCTCTTCAGGACAGAGTAATGGAAGAAACCAAAGAGAAGAAAAATGCTGTGGAAGCTTATGTCTATGACATGCGTAACAAGgtatgtggag--------atgcatgccttgatggttttcct-tgtgatataaacagtatctaatgtccttttttattgtatttag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag-----
 |||||||| ||||| |||||| ||||||| ||||| ||||| || || || ||   ||| ||||| |||||| ||||||||||||| ||| ||||||| ||||| | |       |  |||| | ||| |  ||     | | ||   |||| | ||||    |      | ||||| | |||      
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTCATGGAGGAAACGAAAGATAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgaggattgccatggttttcttgttatttgaggtcaatttttttat--ttttaattattactaaaactaatttcttgatatcattttag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatat-gtaaagttttgagtattgagtactgacgtgtcttgttttcag
 |||||||| ||||| |||||| ||||||| ||||| ||||| || || |||||   ||| ||||| || ||| ||||||||||||| | | ||||||| ||||| | |       |  |||| | |||   || ||| || | |||   ||   |  | | | | || |    |  |  ||||||
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTGATGGAGGAAACAAAGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattgccatggttttcttgttattta-aggatgaattttgtattattactaaaactaatttctca----ttatcatttcag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttt---tgagtattgagtactgac--gtgtcttgttttcag------------
 || ||||| ||||| |||||| |||||||  | || |||||||| || || |||  ||| ||||| |||||| ||||||||||||| ||| ||||||| ||| |   | | | |||| |||| || |   |||  |  | |  | || |     ||  | |    || |      | | || ||||| |            
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggtgttatctttttcttcttctcttactcagggtcta-acatcaactacaaatgcctgtcatataattgttgatttttttttttccgttatcatttcag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G00820.1 (Glycine max), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatg----catatgtaaag---ttttgagtattgagtactgacgtgtcttgttttcag--------
 |||||||| ||||| |||||| |||||||  | || |||||||| || || |||  ||| || || |||||| ||||||||||||| ||| ||||||| ||| |   | | | | | ||  | | |      || |     || ||  |||    | |    || | | |  |||  | | ||  | | |         
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAACGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggcgctatctttcttgttctcttacccagggtctaacatcacatacaaatgcctgtcatataataattgttgattttttttcctgttatcatttcag

upper sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcat-tggcagtat-gcatatgtaaagttttgagtattgagtactgacgtgtc-ttgttttcag------
 || ||||| ||||| |||||| |||||||  |||| |||||||| || || |||  ||||||||| || ||| | ||||||||||| ||| ||||||| || ||   | | |||    |    | |    | | ||  |||| |||||   ||    || ||| ||   ||   |  || | ||| |      
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtg-tttctatcctattggctaagacagaattacagcatttgtaac-cttcacctactga-tatctacacatgattatcttctgccccag

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|125268931|gb|EL283016.1|EL283016
EST:     GGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAA                         CTGAGTGACAAATACCAGGAATATA
genomic: GGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatc ... ttgttttcagCTGAGTGACAAATACCAGGAATATA
EST: gi|124856131|gb|EH940568.1|EH940568
EST:     AGTCTTATGTTTATGATATGCGGAACAAA                         CTGAGTGACAAATACCAGGAATATATC
genomic: AGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatc ... ttgttttcagCTGAGTGACAAATACCAGGAATATATC
EST: gi|125006615|gb|EL078884.1|EL078884
EST:     TATGTTTATGATATGCGAAACAAA                         CTGAGTGACAAATACCAGGAATATATCACTGACTCGGAGAGGGAAGCATTC
genomic: TATGTTTATGATATGCGAAACAAAgtgagaaatc ... ttgttttcagCTGAGTGACAAATACCAGGAATATATCACTGACTCGGAGAGGGAAGCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT