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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactctctgttctagtgattattcttattggttgaatcgaatctcgtctgattattgatgtgatcgagtgtgatgttgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGCTAACACAGAGCGTTATAGCAATGTGGTCGTTGGGATGAACGATACAATG

Basic information

species Arabidopsis thaliana
transcript AT4G39800.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 4
-gttactctctgttctag------tgattattcttatt----ggttgaatcgaatctcgtctgattattgatgtgatcgagtgtgatgt-tgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGCTAACACAGAGCGTTATAGCAATGTGGTCGTTGGGATGAACGATACAATG
 || | | ||||||  |       |||  |   | |      | ||| ||  |   |  | |   | ||||||     | ||| ||| | |   | | |||||||| ||||||||||  |||||||| ||||| ||||| || |||||||| ||||| ||||| || ||||| ||||| |  ||||||||||| || |||
tgtgattttctgtttgacatgaactgacaaaattcagcaaaagtttgtatgtacattaattttggttttgatggacatgggtgggatttgttggtataagGGAGTTCAAGGAGAAGAGCAAGGTGGACAAGGTGGTGGTGCTGTGGACGGCCAACACGGAGCGGTACAGCAACGTGGTGGCCGGGATGAACGACACCATG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 4
------gttactctctgttc--tagtgattattcttattggttgaatcgaatctcgtctgattattgatgtgatcgagtgtgatgttgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGCTAACACAGAGCGTTATAGCAATGTGGTCGTTGGGATGAACGATACAATG
      || |   ||  ||   ||   || | |||||    | |||| |  | |  |    ||  |||| |  |   || ||||         ||||||||||||||||   |  |||||||||||||| ||||| || ||||| || ||||||||||| || || ||| || | || ||  |||| || || || 
gtagtcgtaatcttcaatttcttaaacatgaatcttaaaaatggaatgggcttttcttctttt-ctgattttgt-atgtatgat---------tagGGAGTTTAAGGAGGCAACCAAGGTGGATAAGGTGGTGGTGCTGTGGACTGCCAACACAGAGCGATACAGTAATTTGATTGTGGGACTGAATGACACCATA
















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|125307006|gb|EL321091.1|EL321091
EST:     CATCAAGGACATGAG                         GGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
genomic: CATCAAGGACATGAGgttactctct ... tgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
EST: gi|47829323|gb|CK119007.1|CK119007
EST:     ATCAAAGGTACCAAGAAGGAACAAGTCGACCACATCATCAAGGACATGAG                         GGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
genomic: ATCAAAGGTACCAAGAAGGAACAAGTCGACCACATCATCAAGGACATGAGgttactctct ... tgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
EST: gi|125260984|gb|EL275069.1|EL275069
EST:     ATCAAAGGTACCAAGAAGGAACAAGTCGACCACATCATCAAGGACATGAG                         GGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
genomic: ATCAAAGGTACCAAGAAGGAACAAGTCGACCACATCATCAAGGACATGAGgttactctct ... tgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
EST: gi|125137453|gb|EL177308.1|EL177308
EST:     TCGACCACATCATCAAGGACATGAG                         GGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC
genomic: TCGACCACATCATCAAGGACATGAGgttactctct ... tgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatcgaatctcgtctgattattgatgtgatcgagtgtgatgttgaatcttagGGAGTTTAAGGAGAAGAATAAGGTGGATAAGGTTGTGGTTCTCTGGACGGCTAACACAGAGCGTTATAGCAATGTGGTCGTTGGGATGAACGATACAATG
                     tattgat  putative branch site (score: 3)
                   attattgat  TA-rich tract