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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagttatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC

Basic information

species Arabidopsis thaliana
transcript AT5G52650.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52650.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G43110.1 (Glycine max), 3'ss of exon 2
gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagttatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC
                                                                                                                 ||    ||||||   | |    | |  | ||  ||||    | ||     ||| |  ||| | |  |||  | |||||    |||| ||||||||||||||||||||||| |||||||| || ||||| |||  ||| ||||| || || || || ||||| ||||| |||||||| ||||||||
-----------------------------------------------------------------------------------------------------------------gtccgttagttaacattg----tctcctcttgtgctttacggttg-----tgtttaaattgtaacgtgtgtt-tgatt----cagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCGAAGCACCCGGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: AT5G52650.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G02410.2 (Glycine max), 3'ss of exon 2
gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagttatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC
                                                                                                                 ||    ||||||   | |   |  |  | ||  ||||   || ||     |||    ||| | |  |||  | || ||  | |||| ||||||||||||||||||||||| |||||||| || ||||| ||   ||| ||||| || || || || ||||| ||||| |||||||| ||||||||
-----------------------------------------------------------------------------------------------------------------gtccgttagttaacattgttgtc-tcctcttgtgctttacagttg-----tgttaaaattgtaaggtgtg-tgtgtttgattcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: AT5G52650.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagttatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC--------------------
                                                                                                                 ||    ||||||   | |   |  |  | ||  ||||   || ||     |||    ||| | |  |||  | || ||  | |||| ||||||||||||||||||||||| |||||||| || ||||| ||   ||| ||||| || || || || ||||| ||||| |||||||| ||||||||                    
-----------------------------------------------------------------------------------------------------------------gtccgttagttaacattgttgtc-tcctcttgtgctttacagttg-----tgttaaaattgtaaggtgtg-tgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA

upper sequence: AT5G52650.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G37470.1 (Glycine max), 3'ss of exon 2
gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagttatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC
                                                                                            ||   |     |  | ||      ||  |  |  | | |  |   | | || | | ||  |   ||||  ||   ||  |  |    |||| |||| |    ||||| ||||||||||| ||||||||||| |||||| | || ||||| ||   |||||| || || || || || ||||||||||| |||||||||||||| ||
--------------------------------------------------------------------------------------------gtaggtgccttagcatttatcacgaatcatcttcgttcgttagggttacgtctcg-ttgaacaatgaatcttacctt--tcgttg-gtgtt-tatggt----gcagAGGGAGTTTGCTTCGCGAAGAAGGACTTCAATTTGGCCAAGCACCCTGAGATCGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

upper sequence: AT5G52650.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G02070.1 (Glycine max), 3'ss of exon 2
gttcgttcttcttaaatttgttcttagatctctgttttcttcagcttctgtgagtaaattgattcatttttaggcttatgccgatgaacattgtgatttttgaactagtttaggttaactagt-tatggtagcaattatgatgtttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC
                                                                                                              |||||    |||  | |  | |   ||| |   | | | ||  |   ||||  ||   ||  || |      |  ||   |   |||||| ||||||||||||||||||||||| |||||| | || ||||| ||   ||| || || || || || || ||||||||||| |||||||||||||| ||
-------------------------------------------------------------------------------------------------------------gtaggtgccttagaatttcattggggttacg---tctcg-ttgaagaatgaatcttaccttcttttt------tcttaatgtcggtgcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATTTGGCGAAGCACCCTGAGATTGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

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|47830180|gb|CK119864.1|CK119864
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|152037961|gb|BP804142.2|BP804142
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTGGCTTGGGGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|47830738|gb|CK120422.1|CK120422
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|152033829|gb|BP817117.2|BP817117
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|152034920|gb|BP840005.2|BP840005
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|47828157|gb|CK117841.1|CK117841
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|47831024|gb|CK120708.1|CK120708
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|125305973|gb|EL320058.1|EL320058
EST:     CTGCAAGTACCTCTTCAAAG                         AAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
genomic: CTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGA
EST: gi|164108574|gb|EL994714.1|EL994714
EST:     ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAG                         AAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCT
genomic: ATTATCTCAGAGGCTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGgttcgttctt ... atttttgcagAA-GGAGTTTGCTTTGCGAAGAAGGATTTCAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcttagaaggtgaacattgtgttgattatcatatgttctatgatttttgcagAAGGAGTTTGCTTTGCGAAGAAGGATTTCAATCTTGCTAAGCATCCGTTGATCGATGTCCCCAACCTACAAGTGATTAAGCTTATGCAGAGTTTCAAATC
                      tgttgat  putative branch site (score: 4)
                                              tttttgc  putative PPT
                           attatcatat  TA-rich tract