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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatccttttacatgacctagtctcagctttaattgctaatccctcttaataccatatttggctctacgaaaataaaggacgcagcattgcatagtttttcttgactttaagattctttttac

Basic information

species Arabidopsis thaliana
transcript AT3G04820.1
intron # 10
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G173137_T01 (Zea mays), 5'ss of exon 9
TTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttta-catgaccta-gtctcagctttaattgctaatccctcttaataccatatttggctctacgaaaataaaggacgcagcattgcatagtttttcttgactttaagattctttttac
||||||||||||||| ||||||| || | ||| || |||||  |  | | |||||||||||| | ||||||| || |||||||||||||||| |||   ||||||||   |  ||    || || ||    |||   | |  |      |  | |||  ||| | |  |  | ||  |||  || |                                       
TTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAGGAGatatcctacaaatattttatatgtgtccaaattaggagtttgtattcagtcttgccagcttttgtttaaacataactaagtccgtacag------------------------------------

upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G427822_T01 (Zea mays), 5'ss of exon 8
TTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatccttttacatgacctagtctcagct--ttaattgctaatccctcttaataccatatttggctctacgaaaataaaggacgcagcattgcatagtttttcttgactttaagattctttttac
||||||||||||||| ||||||| || | ||| || |||||  |  | | |||||||||||| | ||||||| || |||||||||||||||| |||   ||||||||   | ||    ||       |   |||   | |  |      |  | |||  ||| | |  |  | ||  |||   | |                                       
TTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAGGAGatatcctacaa-atattttatatgtgtccaattaggagtttgtattcagtcttgccagcttttgtttaaacataactaagtctgtac--------------------------------------

upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G173137_T02 (Zea mays), 5'ss of exon 9
TTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttta-catgaccta-gtctcagctttaattgctaatccctcttaataccatatttggctctacgaaaataaaggacgcagcattgcatagtttttcttgactttaagattctttttac
||||||||||||||| ||||||| || | ||| || |||||  |  | | |||||||||||| | ||||||| || |||||||||||||||| |||   ||||||||   |  ||    || || ||    |||   | |  |      |  | |||  ||| | |  |  | ||  |||  || |                                       
TTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAGGAGatatcctacaaatattttatatgtgtccaaattaggagtttgtattcagtcttgccagcttttgtttaaacataactaagtccgtac--------------------------------------

upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA03G40600.1 (Glycine max), 5'ss of exon 10
TTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatccttttacatgacctagtctcagctttaattgctaatccctcttaataccatatttggctctacgaaaataaaggacgcagcattg--catagtttttcttgactttaagattctttttac--
||||||||||||||  | ||||| |||| | | ||||||||| || |  |||| || ||||||  ||||||||||||||| ||||||||||||||    ||||||||||| |||    |  | | |  | |||| | ||||   |||| ||    || |||  |      |  ||||  |      ||||   |  ||| ||||| |    ||  || |||  |   
TTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATGGAGatatcctttt-cattgtttc-tattatatataatggataatg--tcttgattgattaattgcatgctgatagttaaaaaatagcaaattgattaccgttgttcttcataacaatgttatttagatac

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|116457912|gb|EG500504.1|EG500504
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116421231|gb|EG463823.1|EG463823
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116421229|gb|EG463821.1|EG463821
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAA
EST: gi|116457905|gb|EG500497.1|EG500497
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAAACAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457910|gb|EG500502.1|EG500502
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457913|gb|EG500505.1|EG500505
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457903|gb|EG500495.1|EG500495
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAAACAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457908|gb|EG500500.1|EG500500
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457916|gb|EG500508.1|EG500508
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457919|gb|EG500511.1|EG500511
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
EST: gi|116457901|gb|EG500493.1|EG500493
EST:     AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTG                         AAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA
genomic: AGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatcctttt ... ttctttttacAAAGGCATGTAGTAAATGATGCCCGGGAATATTACAAAGAAACTGGTGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAACTGatatccttttacatgacctagtctcagctttaattgctaatccctcttaataccatatttggctctacgaaaataaaggacgcagcattgcatagtttttcttgactttaagattctttttac

- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA