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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagttttgtaataaatttgtttctaaaaatctataccagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG

Basic information

species Arabidopsis thaliana
transcript AT3G13070.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
-----------------gtatgagttttgtaataaat------ttgtttctaaaaatctatac----cagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG
                  |||   | || ||||  ||      |||| | | ||||| ||  |    || |  ||| | |||  ||   ||     | ||||||||||||||||||||| ||||||| || || || |||||  ||||||| ||||| || ||||||||||| || |||||||| || ||  | || || |
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatata-tatatataatattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG

upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
---------------------------gtatgagttttgtaataaatt--tgtttcta--aaaatctataccagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG
                            |||   | || ||||  |||  | |||||   ||||| || ||    |  |    |||   |   |||||     |||||||||||||||||||| ||||||| || || || |||||  |||| || ||||| || ||||||||||| || |||||||| || ||  | || || |
ttgcaaaagccttatcttcattgattgttatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgc-----agGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG

upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------gtatgagttttgtaataaatttgtttctaaaaatctataccagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG
                          |    | ||   |  |  || ||| | |     | | |     |  |    |     ||   | |  | ||||||||||||| ||||||||| | ||||| || ||||| |||||| |||| |||||||| || ||||| ||||| || |||||||| ||||| || |  || |
ttattgacttaatgggcagaagtaaagctatacttagtttttggatctgtgtgtgtgtgtgtgtggataagatgctatcgctgtaataaatctcttgcagGATATGATCGAAAATGTGTTGGAGATAAAAGATACACATGTTAGAGAAGTGATGACACCTCTTGTGGATGTTGTTGCAATTGATGCCAGTGCAACACTTG

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|124891487|gb|EH970389.1|EH970389
EST:     GAATTGAGTGGTGCCATTGAAGAAGAGGAGCAG                         GATATGATTGAAAATGTGCTAGAGATTAAGGA
genomic: GAATTGAGTGGTGCCATTGAAGAAGAGGAGCAGgtatgagttt ... tgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttctaaaaatctataccagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG
     ttctaaa  putative branch site (score: 2)
                                            ttgccct  putative PPT
     ttctaaaaatctata  TA-rich tract