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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttcattgtcgatatatccatctatatttatcagaatctggtttggtctgattgatgtgtattgggaaatggtgtaatgataatggcagCTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCTAGGACGAGTAAGCCTAAACCTCAACCATCGGATGCATCTGGCGATAACCAGATAATCG

Basic information

species Arabidopsis thaliana
transcript AT1G01790.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 18
--gtgtgtttcattgtcgatat--atccatctatatttatcagaatctggtttggtc-tgat-tgatgtgtattgggaaatggtgtaatgataatggcagCTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCTAGGA---CGAGTAAGCCTAAACCTCAACCATCGGATGCATCTGGCGATAACCAGATAATCG
   |  |   || ||     ||  | || | ||  | | |  | ||         |   ||| ||| | |   || | ||||   || | |   | ||||||||||||||||||||||||||| || |||||||| | |||| |||   |||||||  | |||||||||||  | ||| | || |  || |||||||| |   
ccttccggaccagtgagagaattgaaccgtatacttctctttggattattcacaattgcgatctgaagggatatgtggaatgaattatttacttttgcagCTATGTGAAGCAAGCGGAAGCTCCCTTGGCTATGGATTCTCTCGGATCGCGAGTAAATCCAAACCTCAACCCCCTGATTCTTCGGATGAGAACCAGATCA---
















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|124776076|gb|EH866203.1|EH866203
EST:     GATTAACGAGTTCAGAACCCGTCACTTGTCTGAACTGACCGAG                         CTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCTAGGACGAGT
genomic: GATTAACGAGTTCAGAACCCGTCACTTGTCTGAACTGACCGAGgtgtgtttca ... ataatggcagCTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCTAGGACGAGT
EST: gi|125290757|gb|EL304842.1|EL304842
EST:     CAAACACGATTAACGAGTTCAGAACCCGTCACTTGTCTGAACTGACCGAG                         CTATGTGAAGCA
genomic: CAAACACGATTAACGAGTTCAGAACCCGTCACTTGTCTGAACTGACCGAGgtgtgtttca ... ataatggcagCTATGTGAAGCA
EST: gi|86083727|gb|DR379486.1|DR379486
EST:     CAAACACGATTAACGAGTTCAGAACCCGTCACTTGTCTGAACTGACCGAG                         CTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCGAGGACGAGT
genomic: CAAACACGATTAACGAGTTCAGAACCCGTCACTTGTCTGAACTGACCGAGgtgtgtttca ... ataatggcagCTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCTAGGACGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctggtttggtctgattgatgtgtattgggaaatggtgtaatgataatggcagCTATGTGAAGCAAGCGGAAGCTCTCTAGGCTATGGGTACTCTAGGACGAGTAAGCCTAAACCTCAACCATCGGATGCATCTGGCGATAACCAGATAATCG
               gattgat  putative branch site (score: 4)
                                        taatgataat  TA-rich tract