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

TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag

Basic information

species Arabidopsis thaliana
transcript AT4G12590.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgt-----gagttgtatttgaaatgt--ttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag
 || || |  ||||| || ||  | || ||||| |||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||  ||||||||||        ||  |||| || | |  | |||||  | |     |   ||| | | | || |   || |     | |  ||||| |||
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgct-----tcaatatttttcag

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 3
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatt-tgaaatgtttcatctatgtttttgcgttactggtcatttaagaaac-tgatatcacttaccattttgcag---------------------
||| |||| ||| || || ||  | || || || |||||||||||||| |||||||||||||| ||||||||||| || || || |||||  ||||||||||    |||    |  | || || |  | || |      |   |||  | |   |   | |  || |   |   || ||                         
TCCAAAGGAAGACGCGCAGAAGGCTCAGGCAGCCATGTTTTCTGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTATCCATGATAGTTCCTCAGgttctgtgttccgtacactgatttacttgtggtgcactatagttggctaatcgtgtggcattctaccgtatgttatattaacatcataacttgtgtttttgcag

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttca--tctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag--------------------------------------------
||| || ||  | |  || ||||| |||||    ||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||  ||  | ||| | | |  ||   |  |   |||   ||   | ||||            | |  |  |  |||  |                                               
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtg--ttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G08370.1 (Glycine max), 5'ss of exon 1
-TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttca--tctatgtttttgcgttactggtca---tttaagaaactgatatcacttacc--attttgcag-----------------------------------
 ||| |||||  | |  || ||||| |||||    ||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||||| |||||||||||   ||  | ||| | | |  ||   || ||  |||        | |||   |    | |  || |  || ||| |  || |  ||                                    
TTCCAAAGGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCGAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATCATTCCTCAggta--ttaaaattggagtttgacagtcctctggctttagaaactggatcacgctccttgtacttgtttccaattatcagatgtctcactagcatctacttacgttgtttcgtattttttgaca

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 5'ss of exon 3
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtga-gttgtatttgaaatgtttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag------------
||| |||||  | || |||||| | || ||    ||||| |||||||| |||||||| ||||||||||||||||| || ||||| ||||| || || |||||   | |||   ||   |  |    ||||  |||   || |  | |||  | |  |||    || | ||||  ||||  |             
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATACCCCAGgtattgctgtcggtgtttttctgttgctattctttaatgtaatagatcagatgactaacc---attaattactgttttttacccttgtggacag

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttcat--ctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag------------
||| |||||  | || |||||| | || ||    ||||| |||||||| |||||||| ||||||||||||||||| || ||||| ||||| ||||| |||||   |||   | |   | ||   |  ||||  |||   || |  | |||  | |  |||    || | ||||| ||||  |             
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgta--ttgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaacc---attaattaccgttttttacccttgtggacag

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|124842454|gb|EH926891.1|EH926891
EST:     ATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAGCTTCTTCTTCTCTGGATTTGTTGCAG
genomic: ATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
EST: gi|164053653|gb|ES045035.1|ES045035
EST:     GATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
genomic: GATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
EST: gi|125011977|gb|EL084246.1|EL084246
EST:     ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAACT
genomic: ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACT
EST: gi|86079343|gb|DR375100.1|DR375100
EST:     ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA