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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttttcacagtcttgtttcatcttaccaaaaatttggagttggtgctaacactacttgtgatttctgtccatctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCATGGTTTCTTACCATCTTCATTAATATGCTTCCATGGGAAAGTG

Basic information

species Arabidopsis thaliana
transcript AT2G39280.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 8
----gttagttttttca---cagtcttgt--ttcatcttaccaa---aaatttggagttggtgctaa---cactacttgtgatttc----tgtcca-----tctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCATGGTTTCTTACCATCTTCATTAATATGCTTCCATGGGAAAGTG
    || |  | ||| |   || | ||||  || | |  |||||   |||||||    | |||  |       ||||||| ||||     ||| ||     | |||||   |||||||||||||||| |||||||||||||| || ||||| || |||||||| ||  |||| ||  | || |||||||| ||||||||||
gtttgtaaactattttaattcatttttgtcattgaacccaccaactgaaatttgtttctagtgtcacatttcttacttgttattttcttgtgttcactttttttgcagCCAATCATCTAGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG

upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
----gttagttttttca---cagtcttg--tttcatcttaccaa---aaatttggagttggtgctaa---cactacttgtgattt--ctgtccat-------ctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCATGGTTTCTTACCATCTTCATTAATATGCTTCCATGGGAAAGTG
    || |  | ||| |   || | |||  ||| | || || ||   || ||||    | |   |        || |||| ||||   |||  ||        |||||   ||||||| |||||||| |||||||||||||| || ||||| || |||||||| ||  |||| ||  | || |||||||| ||||||||||
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG

upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------gttagttttttcacagtcttgtttcatctt---accaaaaatttggagttggtgctaacactacttgtgatttctgtccatctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCATGGTTTCTTACCATCTTCATTAATATGCTTCCATGGGAAAGTG
                             |||    |||||  | | || |||  ||||   |  |   |||| |  | | | || |    || | ||     |||| || ||||||| |||| || |||| ||| |||||||||||||| || ||||| || || ||||||||| |||| || || ||||||||||||||||||||||
gtttgtttcttgttgcatattttattatcgttgcccttttccaattattattttttctttatatgaggcattttggatggcttcttatttcacctttg-----tgtc-atgtgcagTTAATCACCTGGATTTTCTGGGAGTGCAGGTGGCATGGGTTACTGGACCGTGGTTTCTTTCCATTTTTATGAATATGCTTCCATGGGAAAGTG

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|164196174|gb|ES069374.1|ES069374
EST:     TTACTTCGAGAGAGATTTCCTAAATTGG                         TTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCAT
genomic: TTACTTCGAGAGAGATTTCCTAAATTGGgttagttttt ... ccatctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaaaaatttggagttggtgctaacactacttgtgatttctgtccatctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCATGGTTTCTTACCATCTTCATTAATATGCTTCCATGGGAAAGTG
                    tgctaac  putative branch site (score: 1)
                                      tttctgtcc  putative PPT
     aaaattt  TA-rich tract