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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctactctatgctacaattttcataaacccattgtgctattatggtagatattccctcgccgtattagatcttatagcaactgacaagttttgtgactgtttagttgtatggtttcttcttttattgcagGTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAG

Basic information

species Arabidopsis thaliana
transcript AT5G41880.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41880.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G03200.1 (Glycine max), 3'ss of exon 11
gtttgttctactctatgcta-caattttcataaacccattgt--gctattatggta--gatattccc----tcgccgtattagatcttatagcaactg-acaagttttgtgac-tgtttagttgtatggtttcttcttttattgcagGTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAG
    ||||  || |   ||  |  |||||  | | ||| |||   || | ||| ||     ||| |     ||    || |     | |  |   ||  | |||     | ||   ||| |   |||     ||  |  | ||  ||||||| ||||| ||||| ||||||||||| ||||| ||||| || ||||| |||||||
----gttcatcttttaactggcctttttctcatatccactgttatctttcatgctattaccatttctgcagtcattatactgcccatcaatgtctctatagaagaccaataacaccttttgacttattaagactgttcatgttttagGTTTCTAAACACATGAATCATTTGCTTAAAGCACCATTCTGTGTACATCCTAAAACAG

upper sequence: AT5G41880.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv02s0025g01350.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------gtttgttctactctatgc-tacaattttcata----aacccattgtgctattat---ggtagatattccctcgccgtattagatct---tatagcaactgaca----agttttgtg-actgtttagttgtatggtttcttcttttattgcagGTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAG
                               ||| |  |||    ||  |||| | | | |     || | || |  | |   |   |  |     | |       | |  ||      || | ||     ||      ||||||| |||   |     |    |||||  || |  | |||||||||||||| |||||||||||||| |||||||| || || || || ||||||||||
gtttgtacaatttctgcccttctcaacaaattttttcttaccacttgagtacattgtccttggggtaatcaatcggtccagagtccagacaatggatacaatattctttgggactcaagtacaacattctgcatctggattttgtgcactaactcacactgacctttctgtttgtgcttcagGTTTCAAAACACATGAACCATTTGCTAAAGGCACCATTTTGTGTGCACCCAAAAACAG
















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|164173880|gb|ES059873.1|ES059873
EST:     CGTATCCTCGAATTGATTTGGAG                         GTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCA
genomic: CGTATCCTCGAATTGATTTGGAGgtttgttcta ... tttattgcagGTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaactgacaagttttgtgactgtttagttgtatggtttcttcttttattgcagGTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAG
   aactgac  putative branch site (score: 2)
                                     tttcttcttttattgc  putative PPT
                                     tttcttcttttatt  TA-rich tract