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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgactcttatattctccttgaattcttacatttaaggtcaatgatgctacaattttctacatgatagGATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTG

Basic information

species Arabidopsis thaliana
transcript AT1G08125.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08125.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0017g01120.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtatgtgtgactcttatattctccttgaattcttacatttaaggtcaatgatgctacaattttctac-----atgatagGATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTG
                       ||||| ||  | |  || |   || | |    |   | |||  ||  ||||||| | | ||| | |      || |||||||| |||||||||||||||||||| || || |||||||| || ||||| ||||  |||| ||||
tcatagcagagaattttaagtattatgt-tggttatattaattctctagcacatctctttataacttccctgatgctgccaattttttcttcttgtggtagGATCCCAATTCGAAGCATTTAGGAACTACGGTTTGGGATGCATCAATGGTATTTGTGAAATTTCTG

upper sequence: AT1G08125.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0061g00490.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtatgtgtgactcttatattctccttgaattcttacatttaaggtcaatgatgctacaattttctac-----atgatagGATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTG
                       ||||| ||  | |  || |   || | |    |   | |||  ||  ||||||| | | ||| | |      || |||||||| |||||||||||||||||||| || || |||||||| || ||||| ||||  |||| ||||
tcatagcagaatattttaaggattatgt-tggttatattaattctctagcacatctctttataacttccctgatgctgccaattttttcttcttgtggtagGATCCCAATTCGAAGCATTTAGGAACTACGGTTTGGGATGCATCAATGGTATTTGTGAAATTTCTG

upper sequence: AT1G08125.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ35393 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtgtgactcttatattctccttgaattcttacatttaaggtcaatgatgctacaattttctacatgatagGATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTG
                  |     |||       |   | |||||  |  | |   || |         || ||||||||||||| |||||  | ||||| |||||||||||  ||||  |||||||||||||||  |||
-----------------gtgggtattggtggacaagtctgaaggtagaaaacg---cagtccgtccttggacagGATCCAAATTCCAAGCACGTTGGAACAACCGTGTGGGACTCGTCGGTGGTGTTTGCCAAATTCCTG

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|152035663|gb|BP860254.2|BP860254
EST:     CCTGTACTGTTACCATTGAGGTTTGGGGGCACGAATTAGACTTTGCTCAG                         GATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTG
genomic: CCTGTACTGTTACCATTGAGGTTTTGGGGCACGAATTAGACTTTGCTCAGgtatgtgtga ... tacatgatagGATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccttgaattcttacatttaaggtcaatgatgctacaattttctacatgatagGATCCAAATTCGAAGCATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTG
          ttcttac  putative branch site (score: 2)
                                        ttttctac  putative PPT
        aattcttacatttaa  TA-rich tract