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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAGAAGCCGACTAGGCAATGGGCTGCTTGGACACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcaccttgacgttcttcttctctatgttgttaacctgttatgtgtgtgaaccttctctttgtgttgttttgtag

Basic information

species Arabidopsis thaliana
transcript AT2G36960.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G36960.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G05420.1 (Glycine max), 5'ss of exon 3
---CTAAGAAGCCGACTAGGCAATGGGCTGCTTGGACACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgta----tcaccttgacgttctt-cttctctatgttgttaacctgttatgtgtgtgaaccttctctttgtgttgttttgtag-----
   | || || ||||| ||||| |||||||| ||||| |  ||||| ||||||||||||||||| ||  | || |||||||| ||||||    |  | ||   ||| || | | ||| ||||  |  | | |  | |         | ||  | |   | || |  |      
CTACAAAAAAACCGACCAGGCAGTGGGCTGCGTGGACTCGACAAGAGGAGGAAAGTTTCTTCACCGCGTTACGACAAGTTGGGAAGgtacatttatctttcgtgttgttacatttctgtgtttgtttcttatggtatcataatgattgctgatcgaaatattcttgaatgtag

upper sequence: AT2G36960.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G23840.1 (Glycine max), 5'ss of exon 3
---CTAAGAAGCCGACTAGGCAATGGGCTGCTTGGACACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgta----tcaccttgacgttctt-cttctctatgttgttaacctgttatgtgtgtgaaccttctctttgtgttgttttgtag-----
   | || || ||||| ||||| |||||||| ||||| |  ||||| ||||||||||||||||| ||  | || |||||||| ||||||    |  | |||  ||| || | | ||| ||||  |  | | |  | |         ||||  | |   | || |  |      
CTACAAAAAAACCGACCAGGCAGTGGGCTGCATGGACTCGACAAGAGGAGGAAAGTTTCTTCACCGCGTTACGACAAGTTGGGAAGgtacatttatctttggtgttgttacctttctgtgtttgtttcttatggtatcataatgatttctgatcgaaatattcttgaatgtag

upper sequence: AT2G36960.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G23840.2 (Glycine max), 5'ss of exon 2
-----------------CTAAGAAGCCGACTAGGCAATGGGCTGCTTGGACACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgta----tcaccttgacgttctt-cttctctatgttgttaacctgttatgtgtgtgaaccttctctttgtgttgttttgtag-----
                 | || || ||||| ||||| |||||||| ||||| |  ||||| ||||||||||||||||| ||  | || |||||||| ||||||    |  | |||  ||| || | | ||| ||||  |  | | |  | |         ||||  | |   | || |  |      
GATGTCGTATATAGCTACAAAAAAACCGACCAGGCAGTGGGCTGCATGGACTCGACAAGAGGAGGAAAGTTTCTTCACCGCGTTACGACAAGTTGGGAAGgtacatttatctttggtgttgttacctttctgtgtttgtttcttatggtatcataatgatttctgatcgaaatattcttgaatgtag

upper sequence: AT2G36960.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0040g01460.t01 (Vitis vinifera), 5'ss of exon 2
CTAAGAAGCCGACTAGGCAATGGGCTGCTTGGACACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtat---caccttgacgt--tcttcttctctatgttgt-taacctgttatgtgtgtgaaccttctctttgt--gttgtt--ttgtag
 ||| | ||  ||  ||||||||||||||||||||| |||||| ||||||||||||||||||||  | || |||||||| |||| ||      |||||  |  | || || |  |  || | ||   || |||  ||   |||        | |    ||||  ||| ||
TTAAAAGGCAAACACGGCAATGGGCTGCTTGGACACGTCAAGAGGAGGAAAGTTTCTTCACTGCATTGCGACAAGTTGGCAAGgcatgtttttcttgatatatttttgttattcaacttctatactttgctataggtcctaactgcaagaatatcaactgttaattgcag

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|86069765|gb|DR365522.1|DR365522
EST:     CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAG                         AATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAGG
genomic: CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAGG
EST: gi|86069766|gb|DR365523.1|DR365523
EST:     CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAG                         AATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGG
genomic: CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGG
EST: gi|86069770|gb|DR365527.1|DR365527
EST:     CACATCAAGAAGAGGAAAGTTTCTTAACTGCTCTTCGTCAAGTTGGAAAG                         AATTTTGAGAAGATAACTTCTC
genomic: CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTC
EST: gi|86069767|gb|DR365524.1|DR365524
EST:     CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAG                         AATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGA
genomic: CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGA
EST: gi|86069769|gb|DR365526.1|DR365526
EST:     CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAG                         AATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAGGTC
genomic: CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAGGTC
EST: gi|86069768|gb|DR365525.1|DR365525
EST:     CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAG                         AATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAG
genomic: CACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAG
EST: gi|86069771|gb|DR365528.1|DR365528
EST:     ACATCAAGAAGAGGAAAGTTTCT--ACTGCTCTTCGTCAAGTTGGGAAAG                         AATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAG
genomic: ACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGG-AAAGgtatcacctt ... tgttttgtagAATTTTGAGAAGATAACTTCTCGTGTTCAGAGCAAAAACAAGGACCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAAGAAGCCGACTAGGCAATGGGCTGCTTGGACACATCAAGAAGAGGAAAGTTTCTTCACTGCTCTTCGTCAAGTTGGAAAGgtatcaccttgacgttcttcttctctatgttgttaacctgttatgtgtgtgaaccttctctttgtgttgttttgtag

- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - -  AGAGGA