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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatccttttggatttcgatactgaaactgaatgagcaagtattgaaagacttttttcttggtctgtagaagatttgagcattatgtttctcctgaactttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTGATGCTCGTCCTGATCATATTCTAAATCTCATACACTATGAG

Basic information

species Arabidopsis thaliana
transcript AT2G39080.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G10460.1 (Glycine max), 3'ss of exon 4
atatcctttt-ggatttcga--tactgaaact--gaatgagcaagtat-tgaaagact-tttttcttggtctgtagaagatttgagcatta-----tgtttct--cctgaactttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTGATGCTCGTCCTGATCATATTCTAAATCTCATACACTATGAG
||||||||||   | |||    ||||   | |   | |   ||   || ||   |  | ||| | ||  | |||  |  | || |    ||     || |||   |||  || ||||| ||| || |  || |||||||||| |||| |||||    |||| || | | ||  ||||||||||||| ||||| ||||| ||||||||||||
atatccttttcaaaattcagtttactaggattccaactattcattcatctgggtggttatttctattattatgtttatcagtttatgtctagtgtctgcttccaaccttgacattttaaacAAAGTAGATAAAGGTGCACATGCTTATTGGTTAGAGAAGGGGATAGTCGAATCTCGTCCTGATCACATTCTGAATCTTATACACTATGAG

upper sequence: AT2G39080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G10460.4 (Glycine max), 3'ss of exon 4
atatcctttt-ggatttcgat--actgaaact--gaatgagcaagtat-tgaaagact-tttttcttggtctgtagaaga-tttgagcattatgtttct------cctgaactttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTGATGCTCGTCCTGATCATATTCTAAATCTCATACACTATGAG----------
||||||||||   | |||  |  |||   | |   | |   ||   || ||   |  | ||| | ||  | |||  |  | |||  |  |  ||| |        |||  || ||||| ||| || |  || |||||||||| |||| |||||    |||| || | | ||  ||||||||||||| ||||| ||||| ||||||||||||          
atatccttttcaaaattcagtttactaggattccaactattcattcatctgggtggttatttctattattatgtttatcagtttatgtctagtgtctgcttccaaccttgacattttaaacAAAGTAGATAAAGGTGCACATGCTTATTGGTTAGAGAAGGGGATAGTCGAATCTCGTCCTGATCACATTCTGAATCTTATACACTATGAGGTCAGAATTT
















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|125023704|gb|EL095973.1|EL095973
EST:     AAGTAGTGTTGGAATGTGGAGGGACTGTCCTTAGACTAGCAGGGCTTTAC                         ACAGAAACTAGAGGTGCACATACTTACTGGTTG
genomic: AAGTAGTGTTGGAATGTGGAGGGACTGTCCTTAGACTAGCAGGGCTTTACatatcctttt ... ctttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTG
EST: gi|125102091|gb|EL156980.1|EL156980
EST:     AGTAAGTGTTGGAATGTGGAGGGACTGTCCTTAGACTAGCAGGGCTTTAC                         ACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTG
genomic: AGT-AGTGTTGGAATGTGGAGGGACTGTCCTTAGACTAGCAGGGCTTTACatatcctttt ... ctttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTG
EST: gi|124754421|gb|EH844551.1|EH844551
EST:     AGGGACTGTCCTTAGACTAGCAGGGCTTTAC                         ACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTGAT
genomic: AGGGACTGTCCTTAGACTAGCAGGGCTTTACatatcctttt ... ctttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttggtctgtagaagatttgagcattatgtttctcctgaactttttatacACAGAAACTAGAGGTGCACATACTTACTGGTTGAGTAAGGAGACAATTGATGCTCGTCCTGATCATATTCTAAATCTCATACACTATGAG
 ctcctgaac  putative branch site 
                                             ctttttat  putative PPT
                                           aactttttata  TA-rich tract