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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatag

Basic information

species Arabidopsis thaliana
transcript AT4G29040.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 3
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatataattctactgagatggcaaatcaatgact--tgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatag
 || || |||||||| || ||  ||||||| || || || || ||  |||| || || ||||||||||||||||| ||||| |||||||| |||||||||||  | ||  ||          |   |  |  || |    |||||| ||     || |    | |   ||  ||||  ||  |      ||
CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggtt--gtaaaccgtgcag

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 4
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtg---ggttctgttt-ataaaatag---------------------
||| || || ||||| ||||| ||||| |||||||| || ||||| ||||| || || || |||||||| |||||||||||||||||||| || ||||||||   |   | |  | ||| ||   ||  |   ||  ||   |  |  | ||||  | |||    || |     ||| | | | |  |||  |                     
AATTGAAAGCCTTGATCCAGCCCTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATCAAAACAAGAAGACGCATTTTCCAGgtcggaatgactagttctgtgaaaacatgtttttggttttcactgacatatcttaat-attcctattctacttagttatatctcactaaaaggtcttatacttttgatatttag

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta---atatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatag----------
||| || |||||||| |||||  |||| |||||||| || ||||| ||||| || || || ||||| || |||||||||||||| ||||| ||||||||||||   ||   ||||| |    |      | | | |||  ||     || |||  | |     |    |||||  |||| | | ||   | |          
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtg--ttctttctttagttttgtttttgtttt

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta---atatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttg-tgggttctgtttataaaatag--------------------
||| || || ||||| |||||  |||| |||||||| || ||||| ||||| || || || |||||||| ||||| |||||||||||||| || |||||||||   | || |  |   |   || |  ||  |  |   |||    |  |  |  |  |    | |   |  |   || | |   |||||                       
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 4
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta---atatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggt-tgtgggttctgtttataaaatag-------
||| || |||||||| |||||  |||| || ||||| || ||||| ||||| || || || ||||| || |||||||||||||| ||||| ||||| ||||||   ||   ||||| |    |      | | | |  |  |||| |  |  |  |  |    ||     | || ||||| | | ||   | |       
AATTGAAAGTCTTGATCCAGCTTTGCTACGGCCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTTCAGgtaggcatgactaattttgtgaaagcaatacacctaccatgtgtttgggaaatcttgatggcctggtccatttgtgttctttctttatttttgttttttt

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta-----atatataattctactgagatggcaaatcaatgacttgttcg---aaactttcttgttcattgaggttgtgggttctgtttataaaatag--------------------------------
||| || ||| | || |||||  ||||||| ||||| || || |||||||| || || |||||||| || || || |||||||||||||| || |||||||||      | | |||   ||   | |||  | ||  |  |  | |||     |  | |  ||   | |||             | ||    | ||                                 
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag

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|86082474|gb|DR378233.1|DR378233
EST:     AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
genomic: AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
EST: gi|125048107|gb|EL120376.1|EL120376
EST:     AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGG
genomic: AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGG
EST: gi|124706458|gb|EH797860.1|EH797860
EST:     ATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
genomic: ATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
EST: gi|125060037|gb|EL128714.1|EL128714
EST:     CGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
genomic: CGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG