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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatctaagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA

Basic information

species Arabidopsis thaliana
transcript AT5G19820.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 4
-----------------------------gtatttgtaaagaagttgtgttgcatctattgttttccctacatgc---aactcttgatctaagtctaacataat---ctaaattt---------------gtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA
                              |  || ||  |     | |  ||| | |||   ||   ||| |      |   || ||   ||| ||  ||| |    |||||||               | |||| |||||  |||| ||||||||| | || ||||| || || ||| ||||||| |||||||||||||| ||||| ||  |||||||||||||||| || |
gtaatttgtccatgtataagttagcttaatttcttatagggggagggggacgcaac-attaccttttatacttatcttgatggttaatgagagtttataatattgtgttaaattttggtgtacttgtcttgcagGAGCACTTCAAAAAATACTATGATGCAGTGATGCCATACCTGAAAGCTATTTTAATGAATGCAACTGATAAGTCCAATAGGATGCTTCGTGCCAAGTCTA

upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
gtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatctaagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA
      ||| |  ||  |   |   | |   | ||| |   |  |||  ||||| || |||| |  || |   ||   ||  |||||||||| ||||| || |||||| | |||||||| ||||||||  ||||  | ||||||||||||||||| || ||  | ||| | || |||||||| |
------gtacaagag--gaaatatttttgaaggttttcgggccagca-ttcttgctcaaagttttgca-atcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA

upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
gtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatc--taagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA
||||||    |     | ||||  ||| |   | | |  |  ||    || ||||||  | | |  |  || || |   ||  ||||||||||| ||||| || |||||| |||| ||||| ||||| ||| |||| ||| | |||||||| ||||||||||| || ||||||||||| || ||||
gtattttgtgaacttctttgttcaatcaac-atatgcaatttatttt-cttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA

upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 6
gtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatc--taagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA
||||||    |     | ||||  ||| |   |||    |  ||    || ||||||  | | |  |  || ||     ||  ||||||||||| ||||| || |||||| |||| ||||| || || ||  |||| ||| | |||||||||||||| ||||| || ||||||||||| || ||||
gtattttgttaacttctttgttcaatcaac-atttataatttatttt-cttttgatcactcatttaattattatggtctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATACCTGAAGGCTATATTGGTTAATGCAACTGACAAATCTAACCGTATGCTTCGTGCTAAGTCCA

upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 4
gtatt-tgtaaag-aagttgtgttgcatctattgttttccctacatgcaactcttgatctaagtctaacataatctaa-atttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA
||||| | ||    ||  | || | |   ||| ||||||  || |    |           || ||||||   |  |  ||   |||||||| || ||||| ||||||||| | || |||||||| || ||| | || ||||||||||| |||||||||||||| || ||||||||||||||| |||
gtattatatattttaaaatatgcttccattatggttttct-tataaatgagc---------agcctaacacttttgagtatcaatagGAACATTTCCAAAAATACTATGATGCAGTTATGCCTTACCTAAAAGCAATATTGATGAATGCCACTGACAAGTCTAACCGCATGCTTCGTGCCAAAGCCA

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|164078274|gb|ES196878.1|ES196878
EST:     GCAAGAAGGAGCTTTAACTGCTCTTGCTTCAGTGGCTGATTCATCACAG                         GAACACTT-CAAAAGTACTATGATACTGTCATGCCTTATCTCAAAA
genomic: GCAAGAAGGAGCTTTAACTGCTCTTGCTTCAGTGGCTGATTCATCACAGgtatttgtaa ... aaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttccctacatgcaactcttgatctaagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA
                                  taacataatctaaatt  TA-rich tract