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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccactgtttcatatgctttttcgtcctgagtcaactttgataatatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG

Basic information

species Arabidopsis thaliana
transcript AT3G13690.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 6
gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccact---gtttcatatgctt----tttcgtcctgagtcaactttgataatatcat--cagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
       |||     ||    |||  |  |     || |   ||| |        |||| |  | |    |   ||  | ||||   ||  ||||| |  |  |||||||||||||||||  | ||| ||||||| |||||||| || |||||||| || ||  |||| || ||||| |||||
----acctaatgtctgttgaactcgattgtataggcatcttgtattcttgttaacttcacaatcctaagataaggttgtaagtc--tttcaataatgttctgacagGTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG

upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S336_36V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgtataaatatgg----tcttgctcattca--tcgtaacagcagatatcc--------actgtttcatatgctttt-tcgtc-ctgagtcaactttgataatat---catcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
||||| ||       |    ||||    |||||  | ||  ||     ||  |         | | ||| ||  |||   | |||  ||||  || |||  |  | |    ||||||| ||||||||||| || |||||||||||||| || ||  |    ||||| || ||  | || || || || |||||
gtatgcatcgtagcagaaattcttttcaattcaagtagttccatttcctactcctaagctggcagattcttacacttgagtagtcattgagagaagttttgttctttggatatcagGTGGGAGATTTTGGACTCGCAAGATGGCAGCCAGACGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACTTTCGG

upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccac-tgtttcatatgctttttcgtcctgagtcaactttgataatatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
                    | | |  ||   |     |     || || ||   |   |  |    | | || |  |||   || |   | |    |   ||  |   || ||||||||||||||||||| || ||||||||||| || |||||  |    ||||| || ||  | || || || ||||||||
gtatgtggcgttccacacactgtttcgaacggtaaatgtttctgtttattgtctgaatggccacatgcctattcctaatgtggttaccgacagcacaagtgttttttggat-atcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGG

upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ05818 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccactgtttcatatgctttttcgtcctgagtcaactttgataatatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
                                     | |  | | || ||||    | |      |||   |   |   |||| |        |||||||| |||||||||||||| |||||||| || ||||| ||| | || || || || || || || || ||||||||
-------------------------------------gtaagt-tgcattgttatgaaagagcacgcgtgaagttccggttttgtt-------ccagGTTGGTGATTTTGGTCTAGCTAGATGGCAACCAGATGGAGAACTTGGAGTTGAAACCCGCGTTATTGGCACCTTCGG

upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ34463 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtataaatatggtcttgctcattcatcgtaacagcagatatccactgtttcatatgctttttcgtcctgagtcaactttgataatatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
                                     | |  | | || ||||    | |      |||  ||   |   |||| |        |||||||| |||||||||||||| |||||||| || ||||| ||| | || || || || || || || || ||||||||
-------------------------------------gtaagt-tacattgttatgaaagagcacgcgtgatgttccggttttgtt-------ccagGTTGGTGATTTTGGTCTAGCTAGATGGCAACCAGATGGAGAACTTGGAGTTGAAACCCGCGTTATTGGCACCTTCGG

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|116452044|gb|EG494636.1|EG494636
EST:     GAGACATGCGTCCTAACAACATCCTCATCACTCATGATAATGAGCCACTG                         GTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTA
genomic: GAGACATGCGTCCTAACAACATCCTCATCACTCATGATAATGAGCCACTGgtatgtataa ... atatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTA
EST: gi|164099413|gb|ES206774.1|ES206774
EST:     TCATGATAATGAGCCACTG                         GTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTA
genomic: TCATGATAATGAGCCACTGgtatgtataa ... atatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTA
EST: gi|164049807|gb|ES142874.1|ES142874
EST:     TGCGTCCTAACAACATCCTCATCACTCATGATAATGAGCCACTG                         GTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGG
genomic: TGCGTCCTAACAACATCCTCATCACTCATGATAATGAGCCACTGgtatgtataa ... atatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccactgtttcatatgctttttcgtcctgagtcaactttgataatatcatcagGTTGGAGATTTTGGTCTAGCAAGATGGCAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG
                                     ctttgat  putative branch site (score: 5)
                                   aactttgataatat  TA-rich tract