Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGTGAAACACAGGCAGTGGTCTCCCAGCTTGCTTTTATGCACTGGCTAGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctctggatctcaatttactattttccttacttccaaatactgaaatacatatcatggcctagtggttgcactataaataaaaccttattttgtt...

Basic information

species Arabidopsis thaliana
transcript AT2G37020.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G37020.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G33940.1 (Glycine max), 5'ss of exon 3
AGAAGTGAAACACAGGCAGTGGTCTCCCAGCTTGCTTTTATGCACTGGCTAGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctctgga-tctcaatttactattttccttacttccaaatactgaaatacatatcatggcctagtggttgcac-tataaataa-aaccttattttgtt
|  ||||| || ||| | || || ||   |||| |||||||||||||||| ||||| ||||  ||||||| ||| |  || ||||| |||||||||||||||||||||    | ||||   ||| |  || || |       |||  |  | | |||    | |    || | |   | |  | ||    |  | |||  |  
AAGAGTGAGACGCAGCCCGTAGTTTCGATGCTTACTTTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCTGAGGAAAAACTTGGGTgtatgtcttaatactctcgtgttagttattgccatgtcaatcaatgttttatt-cattaggtaggtaggtaggtatgcatgcatatgttgatgtcattgcg--

upper sequence: AT2G37020.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G36680.1 (Glycine max), 5'ss of exon 3
AGAAGTGAAACACAGGCAGTGGTCTCCCAGCTTGCTTTTATGCACTGGCTAGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctctgga-tctcaatttactattttccttacttccaaatactgaaatacatatcatggcctagtggttgcac-tataaataaaaccttattttgtt--
|  ||||| |||||| | || || ||   |||| | |||||||||||||| ||||| ||||  ||||||| ||| |  || ||||| ||||||||||||||||||| |    | ||||   ||| |  ||  | |     |||  | ||   ||    | | |      ||  || |   ||| ||  |   |||||  |    
AAGAGTGAGACACAGTCTGTAGTTTCAATGCTTACATTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCTGAGGAAAAACTTGGGTgtatgttttaatactctcgtgttagttattggcatgt---caatcaatgttttattctttaggtatgtatgcatgtatgcatagattga-ttttattaagcatt
















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|164037970|gb|ES067265.1|ES067265
EST:     AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGT                         TGAACAGTTTGGAGTTTGGATTGGAGACAGAAGAT
genomic: AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctct ... tgtacttcagTGAACAGTTTGGAGTTTGGATTGGAGACAGAAGAT
EST: gi|86081369|gb|DR377126.1|DR377126
EST:     AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGT                         TGAACAGTTTGGAGTTTGGATTGGAGACAGAAGATTATCTCACTG
genomic: AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctct ... tgtacttcagTGAACAGTTTGGAGTTTGGATTGGAGACAGAAGATTATCTCACTG
EST: gi|116444079|gb|EG486671.1|EG486671
EST:     AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGT                         TGAACAGTTTGGAGTTTGGATTGGAGACAGAAGATTATCTCACTG
genomic: AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctct ... tgtacttcagTGAACAGTTTGGAGTTTGGATTGGAGACAGAAGATTATCTCACTG
EST: gi|86086716|gb|DR382475.1|DR382475
EST:     AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGT                         TGAACAGTTTGGAGTTTGGATTGGAGACAGAAGATTATCTCNCTG
genomic: AGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctct ... tgtacttcagTGAACAGTTTGGAGTTTGGATTGGAGACAGAAGATTATCTCACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGTGAAACACAGGCAGTGGTCTCCCAGCTTGCTTTTATGCACTGGCTAGAAACTGGAACTCTTCTCGTGCATACCGAAGCTGAAGAAAAACTTGGGTgtatgtctctggatctcaatttactattttccttacttccaaatactgaaatacatatcatggcctagtggttgcactataaataaaaccttattttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa