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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagcaaaaacaattattggaaccaaagatggtccactttcttattatagagttaatgaatttgaaaatgatgttgattttttttttttgattatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTGAATTTCCAACCTGGTGAGGCTTTTGTTGTCAGAAACATAGCCAATATGG

Basic information

species Arabidopsis thaliana
transcript AT1G70410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G03990.1 (Glycine max), 3'ss of exon 5
ttagcaaaaacaattattggaaccaaagatggtccactttcttattatagagttaatga----atttgaaaatgatgttg-attttttttttttgat-tatg-gcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTGAATTTCCAACCTGGTGAGGCTTTTGTTGTCAGAAACATAGCCAATATGG
         |   || |    |    | |  |||  |||   | |||   |||| |||     |||    |||  | ||  ||    || || ||    |   ||||||| |||| ||||| ||||| |||||  |||||||||||||||| ||  || |||||||||| |||||||| ||| | ||| ||||||| ||||| ||||
-------tgatgtttttcattatattataaagtcagcttctcttttaataagtttatgttgccattaatgaatactattatataacattcttatggcacacatgcagTTTATGGTATTTGCATGCTCAGATTCGAGAGTTTGTCCATCTCATATTCTGGATTTCCAACCGGGTGAGGCCTTTATGGTCCGAAACATTGCCAACATGG

upper sequence: AT1G70410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G19080.1 (Glycine max), 3'ss of exon 3
-ttagcaaaaacaatta--ttggaaccaaagatggtccactttcttattatagagttaatgaatttgaaaatgatgttgattttttttttttgattatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTGAATTTCCAACCTGGTGAGGCTTTTGTTGTCAGAAACATAGCCAATATGG
 | |   |   |||| |  ||  ||   |        |||| | | |||| ||| ||  | |  |     || ||  | || ||   |||   |   | ||||||| |||||||||||||||| || ||||||||||| ||||| |||||  || ||||| | || ||||| || ||||| ||| |||| || ||||| ||||
gtaacttattgcaataagtttaaaatttattggataacactgtttaatta-agaattgttaa--tcacttattattgtaatgttgcatttcccacacttgcagTTTATGGTGTTTGCTTGCTCAGACTCTCGAGTTTGCCCATCCCACATTCTGGATTTCAATCCGGGTGAAGCCTTTGTGGTCCGAAATATCGCCAACATGG

upper sequence: AT1G70410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G39510.1 (Glycine max), 3'ss of exon 4
---ttagcaaaaacaattattggaaccaaagatggtccactttcttattataga-gttaatgaatttgaaaatgatgttgattttttttttttgattatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTGAATTTCCAACCTGGTGAGGCTTTTGTTGTCAGAAACATAGCCAATATGG
    |      ||  ||| ||  |    ||  |  |  | |   || | | |   | |||| | | | |   | ||  | || ||   |||   |   | ||||||| |||| ||||||||||| || ||||||||||| ||||| |||||  || ||||| | || ||||| || ||||| ||| |||| || ||||| ||||
taacttattgcaatgatttttaaagt--aaagttttttaataaattctcacacttgctaattactcttac--ttattgtaatgttgcatttcccacacttgcagTTTATGGTTTTTGCTTGCTCAGACTCTCGAGTTTGCCCATCCCACATTCTGGATTTCAATCCGGGTGAAGCCTTTGTGGTCCGAAATATCGCCAACATGG

upper sequence: AT1G70410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G03720.2 (Glycine max), 3'ss of exon 6
ttagcaaaaacaattattggaaccaaagatggtccactttcttattatagagttaatga----atttgaaaatgatgttg-attttttttttttgat-tatg-gcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTGAATTTCCAACCTGGTGAGGCTTTTGTTGTCAGAAACATAGCCAATATGG
         |   || |    |    | |  |||   ||   | |||   |||| |||     | | |  |||  | ||  ||    || || ||    |   ||||||| |||| ||||| ||||| || ||  |||||||||||||||| ||  || |||||||||| ||||| || ||| | ||| ||||||| || || ||||
-------tgatgtttttcattatattataaagtcagattctcttttaataagtttatgttgccactagtgaatactattatataacattcttatggcacacatgcagTTTATGGTATTTGCATGCTCAGACTCGAGAGTTTGTCCATCTCATATTCTGGATTTCCAACCGGGTGAAGCCTTTATGGTCCGAAACATTGCTAACATGG

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|125144430|gb|EL180100.1|EL180100
EST:     CTTGCCAAGACTTCAGACCCCAAAG                         TTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTG
genomic: CTTGCCAAGAC-TCAGACCCCAAAGgttttagctt ... attatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTG
EST: gi|124902854|gb|EH976934.1|EH976934
EST:     CTTGCCAAGACTCAGA-CCCAAAG                         TTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTG
genomic: CTTGCCAAGACTCAGACCCCAAAGgttttagctt ... attatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTG
EST: gi|125300682|gb|EL314767.1|EL314767
EST:     TTCAATCATCTTGCCAAGACTCAGACCCCAAAG                         TTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCAATCTCACATCTT
genomic: TTCAATCATCTTGCCAAGACTCAGACCCCAAAGgttttagctt ... attatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCA-TCTCACATCTT
EST: gi|124744545|gb|EH835707.1|EH835707
EST:     TGAAGAATAGTACTTTGTTCAATCATCTTGCCAAGACTCAGACCCCAAAG                         TTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTT
genomic: TGAAGAATAGTACTTTGTTCAATCATCTTGCCAAGACTCAGACCCCAAAGgttttagctt ... attatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTT
EST: gi|125170769|gb|EL194058.1|EL194058
EST:     CTTGCCAAGACTCAGACCCCAAAG                         TTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTG
genomic: CTTGCCAAGACTCAGACCCCAAAGgttttagctt ... attatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTG
EST: gi|125026115|gb|EL098384.1|EL098384
EST:     GAAGAATAGTACTTTGTTCAATCATCTTGCCAAGAACTCAGACCCCAAAG                         TTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCA
genomic: GAAGAATAGTACTTTGTTCAATCATCTTGCCAAG-ACTCAGACCCCAAAGgttttagctt ... attatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagagttaatgaatttgaaaatgatgttgattttttttttttgattatggcagTTTCTGGTGTTTGCTTGCTCTGATTCTCGAGTTTGTCCATCTCACATCTTGAATTTCCAACCTGGTGAGGCTTTTGTTGTCAGAAACATAGCCAATATGG
                                        ttttgat  putative branch site (score: 4)
                                ttttttttttttgatt  CT-rich tract
       ttaatgaatttgaaaa  TA-rich tract