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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagaagcagttgtgtgatcccatttaagacccggaagaagaattcttagtaaaatgttaatgtggcttgtgtttacaagtgtaattttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC

Basic information

species Arabidopsis thaliana
transcript AT2G39670.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g74190.1 (Oryza sativa), 3'ss of exon 5
tttagaagcagttgtgtgatcccatttaagacccggaagaagaattct-tagtaaaatgttaatgtg-gcttgtgtttaca----agtgtaat-tttgaatgtca-agGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
          ||||| |   | ||    |  ||  | | |    || | ||  |||| | |||  || ||||||  || ||    ||  |||| ||     ||   |||| ||||| || |||||   |||| | || |||||||||||||| || |||||||| ||||||||||| ||||||||||| || |||||  | || || |
----------gttgtctctccacaaccca--cctagtacagcgtttatgtacaaaaaagataaattgtgcttgttcttgcacaacagattaatattctggcgttgcagGTTTTGGCCATAGAGGAGACGTTCCAACACAGGGTGACAAATGTAGTGTTCATGGGGATGGGTGAGCCTATGTTGAACCTGAAATCAGTTTTAGAGGCAC

upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G168412_T01 (Zea mays), 3'ss of exon 4
tttagaagcagttgtgtgatcccatttaagacccgga-agaagaattcttagtaaaatgttaatgtggcttgtgtttacaagtgtaattttgaatgtca---------agGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
              |   | | |||   |     | | ||       || || ||    |   | |  |||   |     | || ||  || ||| | |         |||||||||| ||||||||   |||||| || |||||||||||||| || |||||||| ||||||||||| ||| ||||||| |||||||| || || || |
---------gaaccttcaaccacatgagattgttgaacaggtcctccctcagcaacccctctgtctttctt-catccctcaatgcaacgttaaatattatgccattgcagGTGTTGGCCATCGAGGAGACGTTCAAACACAGGGTGACAAATGTTGTGTTCATGGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCAC

upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G168412_T02 (Zea mays), 3'ss of exon 5
tttagaagcagttgtgtgatcccatttaagacccggaagaagaattcttagtaaaatgttaatgtggcttgtgtttacaagtgtaattttgaatgtca---------agGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
                                              || || ||    |   | |  |||   |     | || ||  || ||| | |         |||||||||| ||||||||   |||||| || |||||||||||||| || |||||||| ||||||||||| ||| ||||||| |||||||| || || || |
---------------------------------------gtcctccctcagcaacccctctgtctttctt-catccctcaatgcaacgttaaatattatgccattgcagGTGTTGGCCATCGAGGAGACGTTCAAACACAGGGTGACAAATGTTGTGTTCATGGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCAC

upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G395039_T01 (Zea mays), 3'ss of exon 3
tttagaagcagttgtgtgatcccatttaagacccggaagaagaattcttagtaaaatgttaatgtggcttgtgtttacaagtgtaattttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
               ||  |||| |     ||||    |     || ||  | |    | ||||   | |        || | | |     | |||  |||||||||| ||||||||   ||||||  | |||||||||||||| || ||||| || ||||||||||| ||| ||||||| |||||||| || || || |
---------------gtcctccc-tcagcaacccctctg-----tttttcttcatccctcaatgcaacat-------taaatattacacc-attgt--agGTGTTGGCCATCGAGGAGACGTTCAAATACAGGGTGACAAATGTTGTGTTCATTGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCAC

upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G07450.1 (Glycine max), 3'ss of exon 5
tttagaagcagttgtgtgatcccatttaagacccggaagaagaat-tcttagtaaaatgttaatgtggcttgtgttta--caagtgtaa------ttttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
            ||  | || |   ||  |    |||     ||| |  |   | ||  ||||  | | ||      |  || |  |||      | ||   ||   |||| ||||| || ||||| || |||||| |||||||||||||||| || || |||||||||||||| || ||||| ||||| ||| |||||||||| || |
---------ctctggatcattctcattgtgtttaggattgtaaatgttctgaaacaagcttaactttgtttaccacaagacagggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC

upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 5
--tttagaagcagttgtgtgatcccatttaagacccggaagaagaattcttagtaaaatgttaatgtggcttgtgtt-----tacaagtgtaattttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
   || | | || |    | ||    |||| ||        || |||||| |   ||   |   | ||  |  ||        | ||   | || ||   ||   |||| ||||| || ||||| || |||||| |||||||||||||||| || || |||||||||||||| || ||||| ||||| ||| |||||||||| || |
ggctttggatcatt---atcattgtgtttaggatt----gtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC

upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 5
---tttagaagcagttgtgtgatcccatttaagacccggaagaagaattcttagtaaaatgttaatgtggcttgtgtttacaagtgtaattttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
   ||            | |||   |||      | |  |||     |  ||  | |         ||   |||||||| | | | || | |    ||   |||| ||||| || |||||  | || ||||| ||||||||||||||||| || ||||||||||| || || ||||||||||| || |||||  |||| ||||
aacttctatgtttaagatttgacagcatcagtttcactaaagctctgtgtttctttattcaacttagtacattgtgttttctattttactat---gtgcacagGTCTTGGCAATAGAGGAGATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTC

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|124720056|gb|EH811458.1|EH811458
EST:     GAAAAGGAGGCTTTTCAAGAAATCTGCAGCGCCATGAAATTATTGAGCAG                         GTGTTGGCTATCGAGGA
genomic: GAAAAGGAGGCTTTTCAAGAAATCTGCAGCGCCATGAAATTATTGAGCAGgtttacttct ... gaatgtcaagGTGTTGGCTATCGAGGA
EST: gi|125067238|gb|EL133816.1|EL133816
EST:     GAAAAGGAGGCTTTTCAAGAAATCTGCAGCGCCATGAAATTATTGAGCAG                         GTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTC
genomic: GAAAAGGAGGCTTTTCAAGAAATCTGCAGCGCCATGAAATTATTGAGCAGgtttacttct ... gaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttagtaaaatgttaatgtggcttgtgtttacaagtgtaattttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
           tgttaat  putative branch site (score: 3)
      taaaatgttaatgt  TA-rich tract