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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggaattcttatactattatcttgtactgcagtctcaatccttatttccatgtttcttgattgagaagatttctgacagttatcgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 3
gtttggaattcttatactattatcttgtactgcagtctcaatccttatttccatgtttcttgattgagaagatttctgacagttat-cgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG
   ||  | ||||| ||  |     ||  |    || || |  || ||   ||  |    |||   ||     ||     | | ||  ||||        || ||||||| |||||||||||||| |||||||||||||||   ||  |    || || || || || ||||| ||||||||||||||||||
--gtgatactcttaaaccttctgagtgaccgctggtgtcca--ctcataagcagctagagtgacgcagtcacattgaagtactgatatgtttgcattctgttcagGCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 5
gtttggaattcttatactattatctt--gtactgcagtctcaatccttatttccatgtttcttgattgagaagatttctgacagttatcgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG
        |||| |   ||  || |   | |    |    ||    || |||  |  |   || |       ||||      | || |   | ||  ||  |  ||||||| ||| |||| ||||||||||||||||| ||   |||  ||| ||| ||||| || |||||||| ||||||||||| ||||||
------gcttctcactttaaaatttgtaggaaaataagaacaggatttgtttataattggtttcagctgttggattgagataatttttttgtgaaatataatacagGCTGGGTTTGCTGGGATTGGAGTTGGTGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 5
gtttggaattcttatactattatcttgtactgcagtctcaatccttatttccatgtttcttgattgagaagatttctgacagttatcgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG
| ||   | | | | | |  ||    | |    |    ||    ||||||  || |   |  ||      ||||      | || |   | ||  ||  |  ||||||| ||| |||| ||||||||||| ||||| ||   |||  ||| ||| ||||| || |||||||| ||||||||||| ||||||
gcttctcactttaaaattgata----ggaaaataagaacaggatttatttatatttggttgcatctgttggattgacataatttttttgtgaaatataatacagGCTGGGTTTGCTGGGATTGGAGTTGGCGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 5
gtttggaattcttatactattatcttgtactgcagt--ctcaatccttatttccatgtttcttg-attgagaagatttctgacagttatcgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG
        |||| |   ||  || |  ||    | |  |   ||  || |||    |||  ||| |       ||||      | || |   | ||  ||  |  ||||||| |||||||| ||||||||||| ||||| ||   |||  ||| ||| ||||| || || ||||| ||||||||||| ||||||
------gcttctcactttaaaat-tcataggaaaataacatgattttttttttatagttggttgcagctgttggattgacataatttttttgtgaaatataatacagGCTGGGTTTACTGGGATTGGAGTTGGCGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 6
------------------------gtttggaattcttatactattatcttgtactgcagtctcaatccttatttccatg-tttcttgattgagaa-----gatttctgacagttatcgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG
                          |   | |   ||   | ||      |  || |   |   |  ||| | | |   |||  | |||   |        |||||   |  | |   |||   || ||  ||||||| |||||||| ||||||||||||||||| ||   |||  | ||||| |||||||| || ||||| ||||| ||||||||||||
gtaagttctgttacatgacttgcccatataagtggataagtttttgctcctttttgtaaattttgtgattaatccaaaaattttcttattattagtcgttactttctacaacatgtttgttacatattttgcagGCTGGTTTTACTGGGATTGGAGTTGGTGCTGCTTACTATGGTCTTAAGCCTGTTGTAGAGTTCATGACATTTAATTTCTCTATGCAG

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|125165356|gb|EL191675.1|EL191675
EST:     TGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG                         GCTGGATTTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCC
genomic: TGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAGgtttggaatt ... catgttttagGCTGGA-TTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCC
EST: gi|125237836|gb|EL251921.1|EL251921
EST:     AGAGTTTACGATACCCCTATTACTGAG                         GCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCC
genomic: AGAGTTTACGATACCCCTATTACTGAGgtttggaatt ... catgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCC
EST: gi|116443796|gb|EG486388.1|EG486388
EST:     TTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG                         GCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCC
genomic: TTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAGgtttggaatt ... catgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCC
EST: gi|125294944|gb|EL309029.1|EL309029
EST:     TTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG                         GCTGGACTTACTGGAATTGGAG
genomic: TTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAGgtttggaatt ... catgttttagGCTGGATTTACTGGAATTGGAG
EST: gi|116376958|gb|EG419550.1|EG419550
EST:     TTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG                         GCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCC
genomic: TTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAGgtttggaatt ... catgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgtttcttgattgagaagatttctgacagttatcgtttaaccatgttttagGCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG
                                              atgtttta  TA-rich tract