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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactcgtctagttttcgttatcctggtccagtagtttgtaagacttctcactgattccgaacctcttatgttggaacaactgcttttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGG

Basic information

species Arabidopsis thaliana
transcript AT1G79650.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g08300.1 (Oryza sativa), 3'ss of exon 9
gtaagactcgtctagttt---tcgttatcctggtccag--tagtttgtaagacttctca---ctgattccgaacc-----tcttatgttggaacaactgcttttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGG
     | |  ||| ||||     |||  | || |   |  ||  |||||   | |   |   || |||  | | |      || || || |  |   |  |  |||||  |||| ||||| ||||||||  | ||| | || ||||||||||||||| | ||||| || ||||| |  ||||| ||||||||| |||||||||||| ||| |
--gtcatttatcttgtttgacatgtttacatgctatggattatcttgtatagcctgctatggcttattttgtatcacctgcctaatctttgtgctggta-tcatgttat-agCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG

upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 9
gtaagactcgtctagttttcgttatcctggtccagtagtttgtaagact-tctcactgattccgaacctcttatgttggaacaactgcttttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGG
         ||||    ||  || ||   ||  |  | ||   | | || | | | || |||| |   | ||| | ||   |  ||| |  |||||| |||||||||||||||| ||||| ||||| |||||||| ||| | ||  ||||||| ||  |||| |||||||||||||||||  | ||||| ||   ||| |
---------gtctg---tttattttctcagtggatgacttccaatgcctcttttaatgtttccaag--tgttaagctgcttcttctgttactgttac-agCCCATGCTTCAGGAGCTTGGCAAGCAGAACCCTCATCTTTTAAGATTAATTCAGGAGCACCATGCAGAGTTTCTTCAGTTGATCAATGAACCTCTTGAAG
















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|116469868|gb|EG512460.1|EG512460
EST:     TTCCAACAATTACGCACCATGGTCCATTCCAACCCTCAAATTCTTCAG                         CCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATT
genomic: TTCCAACAATTACGCACCATGGTCCATTCCAACCCTCAAATTCTTCAGgtaagactcg ... ttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATT
EST: gi|163987194|gb|ES134926.1|ES134926
EST:     TTCCAACAATTACGCACCATGGTCCATTCCAACCCTCAAATTCTTCAG                         CCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTC
genomic: TTCCAACAATTACGCACCATGGTCCATTCCAACCCTCAAATTCTTCAGgtaagactcg ... ttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTC
EST: gi|116469869|gb|EG512461.1|EG512461
EST:     TTCCAACAATTACGCACCATGGTCCATTCCAACCCTCAAATTCTTCAG                         CCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATT
genomic: TTCCAACAATTACGCACCATGGTCCATTCCAACCCTCAAATTCTTCAGgtaagactcg ... ttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacttctcactgattccgaacctcttatgttggaacaactgcttttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGG
                                       ctgctttt  CT-rich tract
                                           ttttgtta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactcgtctagttttcgttatcctggtccagtagtttgtaagacttctcactgattccgaacctcttatgttggaacaactgcttttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA