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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttattgacacagcttttaacgaattcattcttggagtatgacatgttctcgttctctgtagGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT

Basic information

species Arabidopsis thaliana
transcript AT1G09840.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
-------------gtaagt--tttattgac--acagcttttaacgaattcattcttggagtatga--catgttctcgttctctgt-agGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT
              |||||  | | |||    |  |    ||  |  ||   || |  ||| | |  ||||| ||  |  |   | |||| ||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||| || ||||| |||| |||||| |||||||| || |||||||
gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT

upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
-------------gtaagt--tttattgac--acagcttttaacgaattcattcttggagtatga--catgttctcgtt-ctctgtagGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT
              |||||  | | ||     |  |    ||  |  ||   || |  ||| | |  ||||| ||  |   ||  ||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||||  ||||| |||||||| || |||||||
gtaagatattgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT

upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 6
---------------------gtaagttttattgacacagcttttaacgaattcatt-cttggagtatgacatgttctcgttctctgtagGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT
                     || | |  |  || ||     |        |||||| ||||  ||  | ||  ||  |||| | |  |||||||||||||||||||||||||||| ||||| || ||||| || ||||| ||||||||||| |||||||||| |||||| || ||||| || ||||| |
gtaaattttcatccagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttat-cagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCCCCAGAACTCATATTTGGTGCCACTGAATATACGACTGCTATAGATATTT

upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttttattgacacagcttttaacgaattcattcttggagtatgacatgttctcgttctctgtagGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT
|| |||  | | ||      || |      ||||   |||  |||  || |||| | ||| |   ||||| ||||| ||||| ||  | |||||||| ||||| |||||||| || || || || || ||||| |||||||  ||||||||||| ||||||||||| |
gtgagtgctgtcgaattcctttct------ttcacgtttgatgta-aacttgttttggttttt--tagGTGAAAGGGGAACCGAACATCTCTTACATATGTTCCAGATACTACCGAGCGCCCGAGCTGATTTTCGGTGCCACGGAATACACAACAGCAATTGATATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacagcttttaacgaattcattcttggagtatgacatgttctcgttctctgtagGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT
       ttttaac  putative branch site (score: 2)
                                     tgttctcgttctct  putative PPT
               aattcatt  TA-rich tract