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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctaatctaccttttgttcttgagattttgtttctatatctgtagttgaaattgaaattgatgaaatcttggttgtgtttgggaaagTGTTGTTGGATTGAACTTCGACTTCGTGATGTTGAATTTGACAAAGCACTCGTCGTATATGATCTACAATGTCTGCCTCTACTTTAGTCCTGTTATTCAA

Basic information

species Arabidopsis thaliana
transcript AT5G40670.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 1
--------------gtaatctaatctaccttttgttcttgagattttgtttctatatctgtagttgaaattgaaattgatgaaatcttggttgtgtttgggaa---agTGTTGTTGGATTGAACTTCGACTTCGTGATGTTGAATTTGACAAAGCACTCGTCGTATATGATCTACAATGTCTGCCTCTACTTTAGTCCTGTTATTCAA
               |  |||    |   || ||||||     || | ||  |   | |    |||| |||  | | | |     ||| |   ||||    ||   |||||||| || ||||||||||| |||||| || | || ||||| ||||| ||||||||| |||| ||||| |     |||||||||||  ||| | | || 
gtttcttttttttttttttctggatt-ttttctgttctatcctttctcttctttcgttttctcttgagattctagtagttacttacttagaattgttgataaacgtagTGTTGTGGGGTTGAACTTCGATTTCGTGGTGCTCAACTTGACGAAGCATTCGTCGTATTTGATATACAACGCGGTTCTCTACTTTAGCTCTGCTGTCCAG
















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|152035112|gb|BP844984.2|BP844984
EST:     TGGTCAATTAGCTTTTACCCACAGCTGATTTTGAATTTCCGTAGGAGAAG                         TGTTGTTGGATTGAACTTCGACCTTCGTGATGTTGAATTTGACAAAGCACT
genomic: TGGTCAATTAGCTTTTACCCACAGCTGATTTTGAATTTCCGTAGGAGAAGgtaatctaat ... tttgggaaagTGTTGTTGGATTGAACTTCGAC-TTCGTGATGTTGAATTTGACAAAGCACT
EST: gi|124991278|gb|EL063547.1|EL063547
EST:     TACCCACAGCTGATTTTGAATTTCCGTAGGAGAAG                         TGTTGTTGGATTGAACTTCGACTTCGTGATGTTGAATTTGA
genomic: TACCCACAGCTGATTTTGAATTTCCGTAGGAGAAGgtaatctaat ... tttgggaaagTGTTGTTGGATTGAACTTCGACTTCGTGATGTTGAATTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatatctgtagttgaaattgaaattgatgaaatcttggttgtgtttgggaaagTGTTGTTGGATTGAACTTCGACTTCGTGATGTTGAATTTGACAAAGCACTCGTCGTATATGATCTACAATGTCTGCCTCTACTTTAGTCCTGTTATTCAA
                       aattgat  putative branch site (score: 4)
             ttgaaattgaaatt  TA-rich tract