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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G66880.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 3
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
      ||  || | |||||       | || |  | | |   | || |  || |   |     | |||  ||         | ||  |  ||| |   | |   |||| ||||| |||||||||||||| |||||||| || |||||||| ||||| |||||||||||||| ||||| |||||     ||||||||||||| |||
-ctgtgcatgtg-tcttgtttagcc--tttcggggaatttgtgcctg-gaatcttttttaactttattctgatc--------atgtcatgacttttttttcttcatttgtcagTCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatg-tgtttttaaagtgtt-tgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
            | |||  | |  | ||   |  ||      ||||  | |   |   |    ||||   | || ||  |  | | | || | ||  ||| ||    |||  ||||| || |||||||||||||||||||| ||||| ||||| ||||| || || || |||||||| ||  ||||     | ||||| ||||| |||
------------acttt-ctgtagtagtgaaaagaagagagaactttcgctagatttttctcgatgt--gattgctgcctggataatattgtactgttgctttctgattttgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
gtatcacaaatgattt--tgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
           |  ||  ||||     | ||  || |     |    | || |       ||||||  |||   |    |   ||     |   || | ||||   |     ||||| |||||||||||||| ||||| |||||||||||||| || ||||| || || || || || || ||| |     | |||||||||||||||
-----------ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctct----gcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
          |    | ||   |||   |  | | |  || || |  |  | |     || |  | || |  | | ||||       | || ||     | |  |||   |||||||| || |||||||||||||||||||||||||| || ||||||||||| || |||||||| ||| ||||    || || ||||||||||||
----------tacaatagtggatttacaactatagatgat-cattgtt--tcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
     | |   ||||||       | |    |  || | |    |||| |||       | | |  ||    | | |    ||  |||||| |  ||   |||       |||||||| || |||||||||||||||||||||||||| || ||||||||||| || |||||||| ||| || |    || || ||||||||||||
-----atagtggattttacaacaatagatagatgaattgt----ttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcc----cagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 5
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
          |  ||| || ||||  ||||   |   |||    ||   |    |  |||||  || |||| | | | | |   |    ||     |  ||| || ||| |||||||| || |||||||||||||| ||||||||||| || ||||| ||||| || |||||||| ||| ||||    || || ||||||||||||
-------tttttctttcgtccttt--gtattctattttat---tttaaagaatttgaattgttttgatcaatt-tctgtatcctgcaaatgtaatagattttgttattggcagTCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatg-tgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
       ||||     |  ||  |  |||  || ||  | ||| |   ||| | |  || ||  || |||| |  | | |   |    | |  |   |  ||| || ||| |||||||| || |||||||||||||| ||||||||||| || ||||| ||||| || |||||||| ||| ||||    || || ||||||||||||
-------aaatagaggtcatccat--gtacaagtaatgacaca-tcaaggtccattaatagt--tgatcaattactatatcctacaaatctaata--gattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
           |  | ||| | |  |   |||     ||| || |     ||  ||    || ||  |   ||   || |||     |    |    || |     ||  |||||||| || ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| ||| |  |  | || ||||| |||||||||
----------agcatctgtacatcagcattcaatgggtattcaatcccctttgttca--cgttatcctaggat-cattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG

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|124929739|gb|EL007258.1|EL007258
EST:     ATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG                         TCTTCTGTTCTTCATTCACAACCAAAG
genomic: ATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgtatcacaaa ... tttttgacagTCTTCTGTTCTTCATTCACAACCAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
                                       catttcttttt  CT-rich tract
           aaatgtgtttttaaa  TA-rich tract