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

gtaagtttcaccgatgattaatgttgtttgttatctatctctacatgtgcttttttctcatacttgaactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G40200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 3
--------------------------gtaagtttcacc-------gatg--attaatgttgtttgttatctatctctacatgtgctt--ttttctcatacttgaactgtt-ttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
                          |||  ||||||        ||||  || |  |   |||   |  |     |  |||  ||    | | || | ||  | ||| | ||||| || ||| |||| ||  ||||||||||||| ||||||||||||||| |||| | | ||| ||| ||| || || | || || || ||||| ||||||||
gtaatatggtagctacaaactaagatgtagatttcacttttacaagatgctatcagagcatttttagaattgaagttttatgcactgagatctttctttctcaatctgctgttagGATTCCCTATTCTTGGGGTTGAGTGGCAAAAAATGGAAAATCCTGATCTGCGAATGGCAACGGGCATGAAACCTGACCAGAAAGGTGTGCGTATTAGAAG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtaagtttcaccgatgattaatgttgtttgttatctatctcta----catgtgcttttttctcata------cttgaactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
                || | |  |  | | |  ||  || ||| |   ||   ||||    ||||   ||| || ||||        || || ||||  ||| || ||  | ||  |  |||||||||| ||||||||||||||||||||||| | | ||||||| ||| || || |||| ||||| || ||  |||||||
aatttttcccttgctttatgatgtaatgctca--aaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
--------------gtaagtttcaccga---tgattaatgttgtttgttatctatctct-acatgtgctttttt----ctcatacttg--aactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
              || || |||  | |   ||          | ||   |   | | | | |  |||     |    | | ||||||  |||| |   ||| || ||  || | || ||||| |||||||||||||||||||||||| | |||||| |  |||| ||| |       || || || || || ||  || |
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatgatagttgccccactacagcgcgtacttgtgaactatgc-agGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16952 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtttcaccgatgattaatgttgtt-tgttatct-atctctacatgtgcttttttctcatacttgaactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
                  ||||  |||  |||  |||    ||||  || | | | ||||     |     | ||  |||||||||  |||| ||  | || ||||| |||||||||||||| |||||||||||| || | || |||| | |  |||| || || || || || |||||
-----------------gtaatactgtcctgtagtcttgattctagctgcgttctattctttccatgttttttttgcagGGTTTCCCATTCTTGGCGTGGAATGGCAGAAGATGGAAAATCCGGATTTGCGGAAGGCAGTCGGGATGGCACCGAATCAGAAAGGTGTTCGCATAAGAAG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16073 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtttcaccgatgattaatgttgtt-tgttatctat-ctctacatgtgcttttttctcatacttgaactgtttt--agGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
                  ||||  |||  |||  | ||   ||||  || | | | ||||  | | ||   | ||||  |||||||||  |||| ||  | || ||||| |||||||||||||| |||||||||||| || | || |||| | |  |||| || || || || || |||||
-----------------gtaatactgtcctgtagtttagattctagctgcgttctattctt-tccatgtttttttttgcagGGTTTCCCATTCTTGGCGTGGAATGGCAGAAGATGGAAAATCCGGATTTGCGGAAGGCAGTCGGGATGGCACCGAATCAGAAAGGTGTTCGCATAAGAAG

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|163975532|gb|ES036512.1|ES036512
EST:     GGTGATTGTACATTTCATTCAAGATTATGAAAAGCATGATAAATACACAG                         GGTTTCCTGTTCTTGGAATTGAGTGGCAAAAGATGGAAAA
genomic: GGTGATTGTACATTTCATTCAAGATTATGAGAAGCATGATAAATACACAGgtaagtttca ... actgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttgttatctatctctacatgtgcttttttctcatacttgaactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
                                              ctgtttt  CT-rich tract
        ttatctat  TA-rich tract