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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT
                      |||  |  ||||      ||   |  |     ||||||   | || || | ||     |    |||    |||| ||  ||     ||||    |  |||| | |||           ||||| || || |||||||||||| | ||||||||| | ||||||||||| |||||  | || |||||||| || ||||| ||||| ||||| ||| | ||||
--------------------caattgaagtgaaacaagcaagctcacctgattttttttattattta-ggcataatctgtattgcatt----ctgatgagtaa-----catct--ataattgtgtattg-----------cagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 27
gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT
                      |||  |  ||||      ||   |  |   | ||||||   |   |  | |  || ||    |||||  | |   |||||   | |||||    |  |||| | |||           ||||| || || |||||||||||| | ||||||||| | ||||||||||| |||||  | || |||||||| || ||||| ||||| ||||| ||| | ||||
---------------------aattgaagtgaaacaagcaagctcacct--gattttttattat---tatttaggcataatctgtattg-cattct-gatgag--taacatct--ataattgtgtattg-----------cagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 27
gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT
                                        | ||| ||||    || |   ||    || ||  |    ||   ||||  |  |    ||  |||| | ||  |     ||   | |  |  || || | ||||| || ||||||||||||||  ||||||| ||||| || ||||| || || ||  ||||| ||| ||| ||||| ||||||||  |||||||||| ||||
---------------------------------------caatctttttt--gtttgtcctcgggagtgatagtatttcaat-ttatttattatatgcatataattgagatttctaaattttcttttcata-tgcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATACGGGCAGACATTGTTCTTGAACTAGCTTGGATGCACAATATGATTGACT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT
                               || |     |   |  |   | ||||||   | || |  |     |    |  ||||  || |        | ||||  ||     |  | ||| |||   |  |||| ||||| || || |||||||||||  | || |||||||| || || |||||||| || |||||| ||||||| |||||||| ||||| ||||||||| | ||||
-----------------------------ttaatgtgggcatggttctaatatctttttgttgaat-ttctgtggtatggtgcttatttttatt--------attttaagtc-----taatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT

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|116461287|gb|EG503879.1|EG503879
EST:     CCGGCGATCATGATCTTGCAGAACAACTTCTCGTCTACTTCATTGAACAG                         GGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATC
genomic: CCGGCGACCATGATCTTGCAGAACAACTTCTCGTCTACTTCATTGAACAGgtatggatag ... ggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATC
EST: gi|125248636|gb|EL262721.1|EL262721
EST:     CCGGCGACCATGATCTTGCAGAACAACTTCTCGTCTACTTCATTGAACAG                         GGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAA
genomic: CCGGCGACCATGATCTTGCAGAACAACTTCTCGTCTACTTCATTGAACAGgtatggatag ... ggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT
          atgaaattta  TA-rich tract