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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG

Basic information

species Arabidopsis thaliana
transcript AT5G52520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 3
----------gtttgttctctatagagctgtggtca---acttgtggagattttttt-------tgtggtactctcctgtga---caaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
             |  ||  |  | |  |    |||   |||||   | |    ||        ||    | |||  ||| |   ||  || |   ||||    | ||||| |  || ||||| ||  | || || | |||||| |  |||||| ||||||| ||||||||||| |||||||||||||   | || || ||||||||||
gtttgttgaatgctaatcattgcacaagttccttcatgcacttgataacacaaattggaaagaatggaagattctaatgtaatatcatctgctccatttttctcttcagGCAATGCAAATGATTGATGTATATACAAAATTTGCATACGAGCAAGCTGCAATCCCTGTTATTCCGGGTCGAAAATCAAGAGTGGAAACGTTTGCTGGTG

upper sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------gtttgttctctatag--agctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
                                                                 | | || |   | ||  |  | | |  ||    || |   || |  ||   |||       |  | |||  |||   |||   |||||||||  |||||||| ||  | || |||| |||||| ||||||||  ||||||| || |||||||||||| |||||||||   |||| || ||||| ||||
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagattctagtgcactacctcatattctccaattgtta---ttgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG

upper sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 5
gtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgatta-gttttgt---attgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
        |  | |    |   |||||  ||   | || |||  |   ||| |  | |      | |||  |  || |||   | ||||||| | ||||||||| || ||||| ||||||||||||| ||||||| ||||||| |||||| || ||||||||||||| ||  | || || ||||||||||
-------gtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG

upper sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 5
----gtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcct-gtgacaaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
      || || ||| |  ||   || | ||  | |    | |  | |  | | |   || | ||||| |    |  |||    | ||||||| | ||||||||| || ||||| ||||||||||| | ||||||| ||||||| || |||||| ||||||||||||| ||  | || || ||||| ||||
gtccacttcttttctgtcaag--atgataaatcttt----actagtataattgcataatcttagtgacga-cattctgttca--actgcagGCTATACAGATGATTGACATCTATACCAGATTTGCGTATGAGCAAGCTGCAATACCAGTTATTACAGGTCGAAAATCTAAAGTGGAAACATTTGCCGGTG

upper sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 5
gtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
|| |      |||  | |||    | |||  |    || ||| || || |    |    |  ||  | |    || |  | |||||||   ||||||||| ||  |||| || | |||||||| ||||||| ||||||| ||||||||| ||||||||||||||||  | ||||| ||||||||||
gtattcatgatatctatctgaaaaccactccta---atctttcttatgttttcttgtctt--catttaacagattgtaaactgcagGCATTACAGATGATTGATGTCTATACAAAATTTGCTTATGAGCAAGCTGCAATACCTGTTATTACAGGTCGAAAATCAAAAGTGGAGACATTTGCTGGTG

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|116443936|gb|EG486528.1|EG486528
EST:     GGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAG                         GCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCA
genomic: GGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctc ... tgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
                                aaatgattagtttt  TA-rich tract