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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatttcgttatgcatcgttgctgtattctcgatgttgagacaacttctcatactcatcctcggataaaatcagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG

Basic information

species Arabidopsis thaliana
transcript AT1G78920.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
-----------------gtag--atttcgttatgcatcgttgctgtattc---tcgatgttgagacaacttctcatactcatcctcggataaaat--cagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG
                 ||    | |       | |   ||  ||| |       ||| |        ||||| |    || | |  |||  |||  |||||||||||||| || || ||||| ||||||||||| ||  | ||| |||||||||| ||  | |||||||||||||| ||  | || |||||  ||||||
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG

upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 11
-----------------------gtagatttcgttatgcatcgttgctgtattctc-gatgttgagacaacttctcatactcatcctcggataaaat--cagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG
                        ||  | |  |||   ||  ||| ||| |  || ||| |        ||||| |    || | |  |||  | |  ||||||||||||||||| || ||||| |||||||||||  |  | ||| |||||||||| ||  | |||||||||||||| || || || |||||  ||||||
ctaaacatatttaagtcactcccctaattattattac-tattattg-tgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG

upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 11
----gtagatttcgttatg-catcgttgctgtattctcgatgttgagacaacttctcatactcatcctcggataaaatcagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG
    || ||      | ||   || |    || ||  |  | |  |    ||| ||  |  | ||  |          |||||||||||||| || |||||||| || |||||||| || |||||  | |||||||||||||| |||||||| ||||||||  | |||||||| || ||||
gtaagtggacactactttgatctcttcatcgtgtttacattctctaactcactgct--tttttatgttaatcaccttacagGTTGATATTGCCATTCCAGAAGTTTTTGTTGGTGGGTTGTTGGGCTCTATGCTTATTTTCCTATTTAGTGCATGGGCATGTTCTGCAGTTGGCCGGACTG

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|125264374|gb|EL278459.1|EL278459
EST:     GAGGTTTCAGCGTTTGCTAATGTGTCTTTCAAAGAG                         GTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTA
genomic: GAGGTTTCAGCGTTTGCTAATGTGTCTTTCAAAGAGgtagatttcg ... ataaaatcagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtattctcgatgttgagacaacttctcatactcatcctcggataaaatcagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG
                                             ataaaatca  TA-rich tract