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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgctttaatgttgtctttgcctataacag

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA14G36540.1 (Glycine max), 5'ss of exon 9
ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtact--gtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgct-ttaatgttgtctttgcctataacag---------------
||||||||| ||||||||| |||| |  ||||  |||||||| ||||| || ||||||||||| ||||| |||||| |   | |       | ||||   | |  ||||||  | |        | | | ||    |  | |    |  |  | |  |  | ||||| |    ||                
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaattatctgtagtatattaaataccccttatgatttttggagccatatttactgcacaaaaatacattcttgctgacttcttgtttgcttcatgcattttaccactaaacag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 9
ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtact--gtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgct-ttaatgttgtctttgcctataacag---------------
||||||||| ||||||||| |||| |  ||||  |||||||| ||||| || ||||||||||| ||||| |||||| |   | |         ||||   | |  ||||| | | |    |   | | | |||   |  | |    |  | || || |  | ||||| |    ||                
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaattatctgtagcatattaaataccccttatatttttggagc-catatttactacacaataatacattcttattgatttcttgtttgcttcatgcattttaccactaaacag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA02G46380.1 (Glycine max), 5'ss of exon 9
ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtact--gtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgct-ttaatgttgtctttgcctataacag---------------
||||||||| ||||||||| |||| |  ||||  |||||||| ||||| || ||||||||||| ||||| |||||| |   | |       | ||||   | |  ||||||  | |        | | | |||   |  | |    |  | || |  |  | ||||| |    ||                
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagtcaattatctgtagtatattaaataccccttatgatttttggagccatatttactacacaataatacattcttattgacttcttgtttgcttcatgcattttacgactaaacag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 10
ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgctttaatgttgtctttgcctataacag---------------------------------------
 ||||||||||| |||||||| |||| |||||  |||||||| ||||| || || || ||||| |||||||||||| | |  |  | | | |||||   |   || |  ||    | |  |         | | |     ||      |||||  | || |    ||                                             
GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTGCCTCCCAATAGGGAAAGCCAAGgtaatttttcaga-tgtttattgaagttccctgaaatgatgttgtggttgaagcaacagccaatgcctgagc-tgttaatcctatcctgttatactgttattgttatatgttttcttatcttctgtctgccattaacag

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|124838813|gb|EH923252.1|EH923252
EST:     CAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG                         ATTGAACGAGAAAGGAAAGGGCGTAACGATAGTAACTTTCTCGAAGAT
genomic: CAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcac ... cctataacagATTGAACGAGAA-GGAAAGGACGTAACGATAGTAACTTTCTCGAAGAT
EST: gi|164013963|gb|ES210207.1|ES210207
EST:     CAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG                         ATTGAACGAGAAGGAAAGGACGTAACGATAGTAACTTTC
genomic: CAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcac ... cctataacagATTGAACGAGAAGGAAAGGACGTAACGATAGTAACTTTC
EST: gi|125126133|gb|EL171473.1|EL171473
EST:     CCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG                         ATTGAACGAGAAGGAAAGGA
genomic: CCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcac ... cctataacagATTGAACGAGAAGGAAAGGA
EST: gi|116376968|gb|EG419560.1|EG419560
EST:     CAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG                         ATTGAACGAGAAGGAAAGGACGTAACGATAGTAACTTTCTCGAAGATGGTC
genomic: CAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcac ... cctataacagATTGAACGAGAAGGAAAGGACGTAACGATAGTAACTTTCTCGAAGATGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtactgtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgctttaatgttgtctttgcctataacag

- - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG