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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttcgacatccataaacttaacccttttgccttctttagtaatggttttgatgaaaacgaaatgtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT

Basic information

species Arabidopsis thaliana
transcript AT5G43810.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 12
----gtattatttcgacatccataaacttaacccttttgccttctttagtaatggttttgatgaaaacgaaatgtttcttg-taatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
    || |   || |  |     |     |    |  |        |  || ||  | |||        | ||||  |||  || |  |||||||| | ||  | || |||||||| ||  | || |||||||| ||||||||  | || |||||||| |||||||| ||||| ||||| |||||||||||
gtgagtgtcggtttggtaattgcatcgcaatttttccttggaatcctcatattg--tgtgaaatgcttaagatgtaacttaatatttgcagGTGATATAAAACGTATATGTGAAACTGACTTGGGGTTGATATCACAATGTTGCTTAACCAAACATGTTTTCAAGATCAGCAAGCAGTACCTGGCAAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 12
----------gtattatttcgac-atccataaacttaacccttttgccttctttagt-----aatggttttgatgaaaacgaaatgtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
            || |||   |   |    | |  ||| |  | | ||   ||||       |||  || | ||   |   || | | | ||||  | ||||||||||| ||| | || ||||||||||| |||||||| || |||||||||||| | ||||| ||||| || ||||| |  || |||||| |||| |||||
taataaatgtacatgattataattgttgggacatataagcaatgttccgagtttaaattctaaatatttataatttcatataactatattttgt--tttcagGTGATCTCAAGCGTATTTGTGAAACCGACCTTGGTTTAATTTCTCAATGTTGTTTGACAAAGCATGTCTTTAAGATCACAAAGCAGTATTTGGCTAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 13
gtattatt--tcgacatccataaacttaacccttttgccttctttagtaatggttttga-tgaaaacgaaatgttt------------cttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
  || | |  | | |||   |  | || ||      |    |   || |   |||   | | |||| | |  | ||            ||| |  | ||||||||||| ||| |||| |||||||| || |||||||| || || ||||| ||||| ||||| ||||| ||||| || |  ||||||||  |||| |||||
-aatcactgattgtcattgcttgagttgacagaagagaacacagaagaataagttccaagttaaaatgcagagctttcatttaaatatcttttgttttcagGTGATCTCAAGCGAATTTGTGAAACTGACCTTGGTTTAATTTCACAATGCTGTCTGACAAAGCATGTCTTCAAAATCACTAAACAGTACTTGGCTAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 13
----------------------------------------------gtattatttcgacatccataaacttaacccttttgccttcttt--agtaatggttttga--tgaaaacgaaatgtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
                                                 ||  ||       || ||    |  |       | | ||   ||| |   |   ||  |   |   |||| | | || |  | ||||||||||| ||| |||| |||||||| || ||||| || || || ||||| ||||| ||||| ||||| ||||| || |  |||||||| ||||| |||||
gtaagccacactacaagattcttatatggtatcaatcactgattgccacttgcttgagttgacagaagagaatacagaggaacatgttccaagttaaaatgcagaattctcatttaaatatcttttttt-tttcagGTGATCTCAAGCGAATTTGTGAAACTGACCTTGGCTTAATTTCACAATGCTGTCTGACAAAGCATGTCTTCAAAATCACTAAACAGTACCTGGCTAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------gtattatttcgacatccataaacttaacccttttgccttctttagt-----aatggttttgatgaaaacgaaatgtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
                                                       | || ||      ||   | |  ||| |  | | |    ||||       |||  |  | ||   |   || | | | ||||  | ||||||||||| ||| | || |||||||| || |||||||| || |||||||||||| | || || ||||| || ||||| |  || |||||| |||| |||||
gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattttcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgt--tttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------gtattatttc-------gacatccataaacttaacccttt-tgccttctttagtaatggtt-ttgatg---aaaacgaaat---gtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
                               | | ||| |           | ||  |  || |   | | |    | || | |  ||||| || |||    |||||  ||   ||| | |||     |||| |||||||||| |   ||||| || |  || ||  |  | |||||||||||| | || |||||||| || ||||| |||||||||||  ||||||||||
gtatgttctccttcaaattacgaaccataaatttaattccccaggaaagtgtgcaggactttcataatgtgttggattttcaatggtggttattaatgtatgaaacgtcatcgcgttgcatgtgtgtgcagGCGATCTTAAGAAACAGTGTGAGACTGTCCTGGGGGTCGTGTCTCAATGTTGTTTGACGAAACATGTATTTAAGATGAGCAAACAGTACTTGGCAAATGT

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|164023154|gb|ES170332.1|ES170332
EST:     CAATATTACCTGATAACAACGGTTCACTTTATG                         GTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTT
genomic: CAATATTACCTGATAACAACGGTTCACTTTATGgtattatttc ... gtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTT
EST: gi|47828868|gb|CK118552.1|CK118552
EST:     GTTAGAGCTTCTGCTGGCAATATTACCTGATAACAACGGTTCACTTTATG                         GTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTT
genomic: GTTAGAGCTTCTGCTGGCAATATTACCTGATAACAACGGTTCACTTTATGgtattatttc ... gtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTT
EST: gi|86072813|gb|DR368570.1|DR368570
EST:     GTTAGAGCTTCTGCTGGCAATATTACCTGATAACAACGGTTCACTTTATG                         GTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTT
genomic: GTTAGAGCTTCTGCTGGCAATATTACCTGATAACAACGGTTCACTTTATGgtattatttc ... gtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccttctttagtaatggttttgatgaaaacgaaatgtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
                    ttttgat  putative branch site (score: 4)
                                       tttcttgt  putative PPT
         tttagtaat  TA-rich tract