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

gtatgtgttttctcatttcccggtaatttccgctaggatttgctagtatctctgaaccaccattgtgtattatgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG

Basic information

species Arabidopsis thaliana
transcript AT1G49820.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G464137_T03 (Zea mays), 3'ss of exon 3
gtatgtgtttt-ctcatttcccggtaatttccgc-taggatttgcta--gtatctctgaaccacca----ttgtgtattatgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG
|||  |   |  || | ||     || |  || | |  | |||| |   |||  |  |||     |    || ||  ||        |||||    || |||||||||||| | || ||||| ||||| || ||||||||| ||||||| ||  ||| |||||| ||||| || |||||||| |||  |
gtaattacctcactgaattgaaattagtggccacctgtgttttgtttctgtacatgggaattgtgactttttttggtttccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTCTATCATGGTGACCGAAGGTTCAACTCAAGTCATTGATCCAGAATTTGGG

upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 3
---gtatgtgttttctcatttcccggtaatttccgctaggatttgctagt---atctctgaaccaccattgtgtattatgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG
    | ||  | |  |  |||      | | |  |||    |||  | ||   || | |     |      | |||  |  ||| ||||||  ||| || || || ||  |||||||||| ||||| || ||||||||||| ||||||||||  || ||||| |||||||| |||||||| ||| | 
gtattgtggctctctttgtttttacccattatatgctgtagtttcgttgttagattttttctttataggaatttatggtcctgt-agGTTCATTGAGAGGGCCCAGGCACTAATACATGGAGATCTACACACTGGTTCTGTGATGGTTACTCGTGAATCAACTCAAGTTATTGATCCAGAATTTGCA

upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G40730.1 (Glycine max), 3'ss of exon 3
------gtatgtgttttctcatttcccggtaatttccgctaggatttgctagtatctctgaaccaccattgtgtattatgttgtt--agGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG
       ||     ||| |  ||| ||  | || | |  |||  |||| |  ||  | |   |    || |    |||||||  |  ||||||  ||| || || || ||  |||||||||| ||||| || ||||||||||| |||||||| |  || ||||| |||||||| |||||||| ||| | 
gtattattactcacttttt--tttacccattatatgcagtagt-tttgttgttagattttttct-ttataggaatttatgttcctgtagGTTCATTGAGAGGGCCCAGGCACTAATACATGGAGATCTACACACTGGTTCTGTGATGGTTACCCGTGAATCAACTCAAGTTATTGATCCAGAATTTGCA

upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------gtatgtgttttctcatttcccggtaatttccgctaggatttgctagtatctctg--aaccaccattgtgtattatgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG
                                            |||| | |  | ||  |    |||||         |   | |   |||  |   || |    ||      ||| |||  ||||||||||| ||| | |||||  || ||||||| ||||||||||||||||| || |||||||| |  ||||| || ||||||||||||||||| |||   
gtactgtttccatatcagtgcctcatttcttgcagtaatataaaatgtttctattaatagcagtttaattctgaaataaacaggttgaaatcctttctaagcctagttagaatctattttgc-agGTTCTGTGAGAGATCGCAAGCCCTAGTACATGGAGATCTTCATACTGGTTCAGTTATGGTTACCCCTGATTCGACTCAAGTTATAGATCCAGAATTTGGC

upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------gtatgtgttttctcatttcccggtaatttccgctaggatttgctagtatctctgaaccaccattgtgtattatgttgt-tagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG
                                            || | | |  | ||  |    |||||         |   | |   |||  |      ||    |  | | | || |  ||||||||||| ||| | |||||  || ||||||| ||||||||||||||||| || |||||||| |  ||||| || ||||||||||||||||| |||   
gtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTCAGTTATGGTTACCCCTGATTCGACTCAAGTTATAGATCCAGAATTTGGA

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|116447257|gb|EG489849.1|EG489849
EST:     GTGCGCGAAGACAGTGCCTTGAAGCTCGAAATCGCAGAACTAAAATCGAT                         GTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTC
genomic: GTGCGCGAAGACAGTGCCTTGAAGCTCGAAATCGCAGAGCTAAAATCGATgtatgtgttt ... atgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTC
EST: gi|116447256|gb|EG489848.1|EG489848
EST:     GTGCGCGAAGACAGTGCCTTGAAGCTCGAAATCGCAGAACTAAAATCGAT                         GTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTC
genomic: GTGCGCGAAGACAGTGCCTTGAAGCTCGAAATCGCAGAGCTAAAATCGATgtatgtgttt ... atgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccgctaggatttgctagtatctctgaaccaccattgtgtattatgttgttagGTTCTGTGAAAGAGCTCAAGCTTTAATACATGGTGATCTTCATACTGGTTCTGTCATGGTTACTCAAGATTCAACGCAAGTTATAGATCCAGAGTTTTCG
                                         tattatgtt  TA-rich tract