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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctttcctcgctgtgcataaactagagaattgcatgacctgtagcatcaaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG

Basic information

species Arabidopsis thaliana
transcript AT5G12200.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
-------------------------------------------------------------------gtttctttcctcgctgt--gcataaactagagaattgcatga-cctgtagcat-caaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
                                                                   ||   ||  |    | |  |     |||      |||||  | | | || | | | ||  | ||  |   |  | |    |   | ||    |  |       ||| |||||||||||||||||||||| ||||| ||||| || ||||| |||||| | ||   |||||||||| | |  || ||||||||||||||||
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG

upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 8
gtttctttcctcgctgtgcataaactagagaattgcatgacctgtagcatcaaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
      ||  | |||| |    || |     ||| | ||   || || |  ||| |  |      || |  | |  |   |   |   ||   | |   | | ||||||||||||| |||||||||||||| ||||| || ||||| |||||| | ||   ||||||||| || |  || || |||||||| ||||
------ttaattgctgagaggcaa-tgttacattacctgctatggagaaggaaacttatgttgcatttttcatagttacataaacacctaactgtactttgt-tgcagCTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATG

upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 8
gtttctttcctcgctgtgcataaactagagaattgcatgacctgt-agcatcaaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
   | ||||   ||| || || | |||      ||  ||  |  | |         |  |||||     ||     |      | |  ||      | || || | ||||| |||||||||||||| ||  | || ||||| || || |||||||| ||| ||||||| ||||| | ||| ||||||||||| ||||
---tgtttctgagctctgtattatctaataccctgtgtgctcaattaattcttttttactaagactgattatttgaccaagggtaccgttt-----acaaccttt-cagCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAGAAAGCTCTTGGAATTGATGACTTCCGGAAAATTCCTAATGGTGTCAATG

upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------gtttctt----tcctcgctgtgcataaactagagaattgcatgacctgtagcatcaaaatgttaagatcttctaaacacctttttctccttt-----tattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
                                                        ||||||     |  || | |   || || || |   ||  |    |  |    ||||  |  |  | | | || | |   ||| | |          ||      | |  | ||||||| |||||||||||||| ||  | || ||||| || ||||||||||  ||| | ||||| ||||| | ||| ||||||||||| ||||
gtttcacattatgattcaggcttaggttcaataaccaattaaagatgagggtttgagtttctcaggatagtctcagc-tatgaaatacacccttcaagcttccctcagctcaattttattcgttttacttagcttgtttatttgaccaaaggatacctttttgaaatttgcagCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAAAAAGCTCGTGGAATCGATGACTTCCGGAAAATGCCTAATGGTGTCAATG

upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 8
gtttctttcctcgctgtgcataaactagagaattgcatgacctgtagcatcaaaatgttaagatcttctaaacacctttttctccttttattggga-----taatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
              | |   | | |   |  ||| | | | | |        || | |   | | ||    | |   |||  |      |  |  |     |||  | ||||||| |||||||||||||| ||  | || ||||| || ||||||||||  ||| | ||||| ||||| | ||| ||||||||||| ||||
----------caattatttctgatc---aatattccctcagcggctcagctcaattttattggttttacttagattgtttatttgaccaaaggataccttttaaaatttgcagCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAAAAAGCTCGTGGAATCGATGACTTCCGTAAAATGCCTAATGGTGTCAATG

upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
gtttctttcctcgctgtgcataaactagagaatt--gcatgacctgtagcatcaaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
       ||  |  || | ||||  | ||   |   |||| | || |   ||    |  ||||  |  |||    |  ||| | |||  | ||  |  |    | ||||||||||||| |||||||| ||  | |||||||| ||||| |||||| | ||| ||||||||||||| | ||| ||||||||||| ||||
-------tctacattgaggataatgttgatcctaaagcataatct-tgatattgttac-ttaaagtgatctttg-aattttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG

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|124880158|gb|EH959060.1|EH959060
EST:     TACGACATGGGAAAGCCCTACAAGATGCCCTTTCCACAGGAATCCTTCAG                         CTTGTAGGAACTGATCACTGCACTTT
genomic: TAGGACATGGGAAAGCCCTACAAGATGCCCTTTCCACAGGAATCCTTCAGgtttctttcc ... atctctgcagCTTGTAGGAACTGATCACTGCACTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG
            ttctaaa  putative branch site (score: 2)
                                              tctctgc  putative PPT
                                ttttatt  TA-rich tract