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

TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgtgcaatagcttccgagctatatctttaccaggactgaaaattagag...

Basic information

species Arabidopsis thaliana
transcript AT3G54840.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgtgcaatagctt----ccgagctatatctttaccaggactgaaaattagag
|||  | || ||||| |||||| | |||||||  | |||  || |||| |||||||||||||| || ||||| || |  ||||||||||||||||| ||||||   | | ||         |    ||   |  |||| | |   | |  |||   | ||  | |     ||| || |   | | |  | |      ||   | 
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctcta---ctcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatcttcttgaagctctgatgtaa-

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 5
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatt-tcgttcatgtttctaggattcgtgcaatagcttccgagctatatctttaccaggactgaaaattagag-
|||  | |||||||| || |||||||| || | |||||| |||||||| ||||||||||||||||| ||||| ||||  ||||||||||| ||||||||||||  |||||||    |  |      |  ||| || ||  |  || |   | |  |   | |  ||  ||   ||||   || ||  |        ||    
TGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttcagttactgtatggttctatattgtcatttcttgttttgttagttatttgaaa--ttttgaatgatatgaataacaaaaaattcccctattat

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgt-gcaatagcttccgagctatatctttaccaggactgaaaattagag-
|||  | ||||| ||||| |||||||| || | |||||| |||||||| ||||||||||||||||| ||||| ||||  ||||||||||| ||||||||||||  ||| |||     |   | ||||| || | ||   |  || |    || ||      |  ||  ||   ||||   || ||           ||    
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagtta--ttgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 5
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgtgcaatagcttccgagctatatctttaccaggactgaaaattagag-------
||| || |||||||| ||||| || || |||| |||||| ||| | |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||||| ||||    |     |  | || | ||    || || | | |    ||| |||   |   |     |||| ||||| |  |        |||           
TGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGTAGTGTATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatctttttttag----taggaagtgcaatagtatttatttctgtttctttcttgcttaattattt---ctatttctttgcttgcttcatttatttatttcttttt

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|124761286|gb|EH851416.1|EH851416
EST:     ATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAG                         GAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCT
genomic: ATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttc ... aatctaacagGAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCT
EST: gi|124887150|gb|EH966052.1|EH966052
EST:     ATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAG                         GAACTGCAAAAGCATGGAAG
genomic: ATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttc ... aatctaacagGAACTGCAAAAGCATGGAAG
EST: gi|124762371|gb|EH852501.1|EH852501
EST:     CCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAG                         GAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCTCTGGTTGGTAAC
genomic: CCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttc ... aatctaacagGAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCTCTGGTTGGTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgtgcaatagcttccgagctatatctttaccaggactgaaaattagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA