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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG

Basic information

species Arabidopsis thaliana
transcript AT5G35910.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 3'ss of exon 3
------gtttttcctgggatacttcaattccattacaaaaggtctaaaatat--attttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
        |  || |     | ||  || |   | || |  ||   |       ||| | |    ||| |   || ||   | |  |||||||||||||| |||||||| ||||| || ||||||||||||||||| ||||||||||| ||||| || ||||||||||| |||
gtataacatgctctttcatcattttcatacatgtgcatattgttatatgctccaattgtgtagattctcattgctcttatggcacatagGTAATGCATGGTGCAGATCGTGATATAATATGGCTTCAACGGGACTTTGGCATATATGTATGCAACCTTTTTGACACAGGCCAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 3
gtttttcctggg-------atacttca--attccattac----aaaaggtcta--------aaatatattttctgtgctct-gaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
|||| | ||| |       ||  || |  |||  |||      |||  || ||        || |  | |||||||   || |   |||  || || ||  ||||||||||||| || ||||| |||||||| ||||| |||||||| |||  ||||||||| |||||||| |||||||||||||||
gtttcttctgcgttctccaattgtttatcattttattgaggggaaattgtttatcattgtgaactcaaatttctgtttacttggtttcttcttgtgcaaaaagGTAATGCATGGGGCTGATCGTGATATTATGTGGCTCCAACGGGATTTCCACATATATGTTTGCAATCTTTTTGACACAGGACAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G118917_T02 (Zea mays), 3'ss of exon 3
gtttttcctgggatacttcaattccat-tacaaaaggtctaaaatatatttt---ctgtgctctgaaatctgt-ttatg-taattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
            || |||   | | ||  |   |   | |  ||  | | |    |||   | |   ||  || |||||  ||  ||||||||||||| |||| ||| ||||| || ||||||||||| |||||| |||||||||| ||||| || ||||||||||| |||
-----gtgcaatatgcttgcttcctatacatttatactttgtaacgtgtctaaaactgcagtttcttattggtcttatgacaaacagGTAATGCATGGTGCAGGTCGTGATATAATATGGCTTCAACGAGACTTCAGCATATATGTGTGCAACCTTTTTGACACAGGCCAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 3
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
||||||      | ||| |||    ||  |   | ||    | |  | |||||| | | | |    |  ||    || |||||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| |||||||||||||||
gttttt----aaaaactacaaaataatgcctctatgt----actcgaatttctg-gttttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 3
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
||||||      | ||| |||    ||  |   | ||    | |  | |||||| | | | |    |  ||    || |||||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| |||||||||||||| 
gttttttt---aaaactacaaaataatgcctctatgt----actcgaatttctg-gttttcattcgttcttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAA

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 4
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
||||||      | ||| |||    ||  |   | ||    | |  | |||||| | | | |    | |||    || |||||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| |||||||||||||| 
gttttt----aaaaactacaaaataatgcctctatgt----actcgaatttctg-gttttcattcgtttttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAA

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G452875_T01 (Zea mays), 3'ss of exon 3
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
||||||      | ||| |||    ||  |   | ||    | |  | |||||| | | | |    |  ||    || |||||||||||||| || ||||| ||||| || ||||| || || ||||||  ||| ||||| |||||||| |||||||||||||||
gttttt----aaaaactacaaaataatgcctctatgt----actcgaatttctg-gttttcattcgttcttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGAGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G29260.1 (Glycine max), 3'ss of exon 3
gtttttcctgggatacttcaattccat-tacaaaaggtctaaaatatattttctgtgctctgaaatctgtttat-gtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
        |  ||| |     ||  || |        |  |  | |  || |   |  | |  | | | ||||| | || ||||| |||||||||||||||||||| ||| | ||||| |||||||| || ||||| ||||| |||||| | || || || || |||
-------gtcagatgcacatgtttgatgtttctttaattcatcagactttcttctttttgttgactttatttattggaaatagGTCATGCATGGAGCAGATCGAGACATTGTGTGGCTGCAACGGGATTTTGGCATTTATGTTTGCAATATGTTCGATACTGGCCAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 4
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgct-ctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
  ||  |     ||| ||   ||   |   ||    |  ||  ||| | |    | ||  ||| || | |   | ||||||||| |||||||| || ||||||||||||   ||||||||||| ||||| || || ||  | || ||| | ||||||||    |||
-gttagctgcacataattggtttttctcttaa----ttcaacttatttgtctcattctgttgacatttatgggt-taattagGTCATGCATGGTGCGGATCGAGATATTGCATGGCTTCAACGAGACTTTGGAATTTACATTTGTAATTTGTTTGACACTCACCAG

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 2
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
|||  ||   |    |||       |||        | |||   || |  |   |        || |   ||  ||||||||| ||||| || |||||||| ||||| || |||||||||||||| || ||||||||  |||||||  | ||||| || ||||||
gttgatctctgt---cttgttgcttatttttggtattataatggatctacttcatttgtgatgatatacctaattaattagGTTATGCACGGGGCAGATCGGGATATCATTTGGCTTCAACGGGATTTTGGCATATACATCTGCAACATGTTTGATACCGGACAG

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|86064860|gb|DR360617.1|DR360617
EST:     AGATATTCAAAGACCCTAAAAAGAAAAAG                         GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGC
genomic: AGATATTCAAAGACCCTAAAAAGAAAAAGgtttttcctg ... atgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGC
EST: gi|116454660|gb|EG497252.1|EG497252
EST:     ACATTGGGCCTTATCTAAGGGAGATATTCAAAGACCCTAAAAAGAAAAAG                         GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGC
genomic: ACATTGGGCCTTATCTAAGGGAGATATTCAAAGACCCTAAAAAGAAAAAGgtttttcctg ... atgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG
         gtctaaa  putative branch site (score: 3)
          tctaaaatatattttc  TA-rich tract