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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaggatcattcaccatcattgtaattttaatcttattgacttgtttattgtgtcaaccttctaaatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG

Basic information

species Arabidopsis thaliana
transcript AT2G02180.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G28990.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------gtttaggatcattcaccatcattgtaattttaatcttatt-gacttgtttattgtgtcaaccttctaaatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
                                                      |    || |||    ||  || |||||  ||| | ||| ||||   ||| ||  |||    |||  ||||||    || | |||||||||| | ||||| |||||||||||  | || |||||||||||||| || || ||||| ||| |||| || ||||||||||| ||||||||||||
gtattggagtatagggaatgtggcatttatttttgagttattttttgaacctaatattaataatttgttatt-ttctaattagaatgtgattagactcacttaatgc-tca---ctctgcatttgc----ttgtgtttgtagATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTATCAG

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G01360.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------gtttaggatca-ttcaccatcattg--taatttt--aatcttatt-gacttgtttattgtgtcaaccttctaaatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
                                                         || ||| | ||    || |||   |||||    ||| |  || ||||   ||||       ||   ||   |||||    |||| |||||||||| | ||||| |||||||||||  | || |||||||||||||| || || ||||| ||| |||| || ||||||||||| |||||||| |||
gtattcgagtatagggaatggaatgtaacatttaatttgagtaattttttcttaacataagattagttgtttattattttctaattacagaatgtggttagactcacttat---actcactcactgcgtttgc----ttatgtttgtagATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTACCAG

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G26630.2 (Glycine max), 3'ss of exon 3
-------------gtttaggatcattcaccatcattgtaattttaatcttattgacttgtttattgtgtcaaccttcta---aatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
             ||||  | |  ||    ||  || |  ||   |  |  || |    || |   |    | ||| ||   |||   |||  |  | | |||||||| | ||||||||||| ||||| || || |||||||||||||| || || ||||| ||  |||| || ||||||||||| |||||||| |||
gtaggaatgatttgtttcagctttttttatatatttttttttaacaattccttcataaattaaggcttattatcttatagctaatgctcagcttcgtgtgtgtagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCACTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 3
--------gtttaggatcattcaccatcattgtaattttaatcttattgacttgtttattgtgtcaaccttcta---aatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
        | || |  |||       |  || |  |||| |  |  || |    || | | | | || ||  ||   |||   |||  |  | | || ||||| | ||||||||||| ||||| || || |||||||||||||| || || ||||| ||  |||| || ||||||||||| |||||||| |||
gtagaaatgatttgtttcagctttttttttttt--ttttcaattcctttataaattaagttttttaatctcatagctaatgctcagcttcgtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------gtttaggatcatt--caccatcattgtaatttt---aatcttattgacttgttt-attgtgtcaaccttctaaatttgcagtgttatctttgt-agATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
                                               |||   ||  ||  ||  || |   | | |||   ||   |||  | |||||  ||||| || |   | |    |||  ||| ||| ||| | ||||| | ||||||||||| |||||||| |||||||||||||||||||| |||||||||||| ||||  | |||||||| ||||| || ||||||
gtctgactgttgttaattcagtttgctctttttaattgttgattaactttgttattgttatcattattacaattacttttagaagtctatccagttgttagattgtttctaatctgttg-cttgttgtggtatttttcttagATTATCCAACATATCTTACTTGATATGCCAAGTCTTGCTTTCTTCACAACCTATGCTCTTTTGGTATTGTTCTGGGCAGAAATATACTATCAG

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S295_28V6.1 (Physcomitrella patens), 3'ss of exon 3
---gtttaggatcattcaccatcattgtaattttaatct---tattgacttgtttattgtgtcaaccttctaa---atttgcagtgttatctt--tgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
   || | |    | ||| |     | |   || || ||   | || | ||      |  |   ||   |  |    | |||  | | ||||   || ||||  |||||||  |  |  | ||| | ||  |  |   ||||||||| || ||| |||||||||| ||||||||||||||||| ||| | |||
gctgtgttgtgaaagtcagctgacgtatgtgttcaaactatatctttaattccaccctccgctcactcaccgattggtgtgcgatctcatctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAG

upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S237_67V6.1 (Physcomitrella patens), 3'ss of exon 3
---gtttagga--tcattcaccatcattgtaattttaatcttatt--gact-tgtttattgtgtcaaccttctaa--atttgcagtgttatctt--tgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
   |||  |||  ||| |   | | || || | |   || ||||   |||| |  |  ||  ||||| |     |   | ||   |||  | |   || ||||  | || ||  |  |  | ||  | ||  |  ||   || |||||||| ||| ||||||||||  | |||||||||||||||||| | |||
tctgttgtggaagtcaatggacgt-atagtgactcgcattttatctggactctagtgcttcagtcaatcactggattgtgtgtgatgtcctttggatgcagATATTACAGCACGTTCTTTTGGACCTGCCGGGCATTTTGTTTTTCACCACATATACTCTTCTGGTGTTGTTCTGGGCTGAAATTTATCACCAG

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|19877197|gb|AU238028.1|AU238028
EST:     GTGCTGTGGTGTTTGTCTTCAGGCGAAATGTTCAGTTTATGCAACCAGAG                         ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACC
genomic: GTGCTGTGGTGTTTGTCTTCAGGCGAAATGTTCAGTTTATGCAACCAGAGgtttaggatc ... atctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattgacttgtttattgtgtcaaccttctaaatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
                           ttctaaa  putative branch site (score: 2)
                                           ttatcttt  putative PPT
                           ttctaaattt  TA-rich tract