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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctatatctcggcctcaattatttgcttccaactgggtctatgcacaataatgcttcttacatctacatttgtttttttttttgtacttttttatgaccagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCATGACTTCCCGGAGTTTCTCTGTGATTATCACTTTACCTTTTGTGATGTTA

Basic information

species Glycine max
transcript GLYMA03G27260.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27260.1 (Glycine max), 3'ss of exon 29
lower sequence: AT1G02080.2 (Arabidopsis thaliana), 3'ss of exon 44
gtttgtctatatctcggcctcaattatttgcttccaactgggtctatgcacaataatgcttcttacatctacatttgtttttttttt--tgtacttttttatgac-cagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCATGACTTCCCGGAGTTTCTCTGTGATTATCACTTTACCTTTTGTGATGTTA
||||||   | | ||  | ||  | |||   || ||   |   |||      ||| |   |  || |  || | | || | ||||||  |||  || || ||  |  |||||| | |||| || ||||| ||| | || ||  |  | || || |||||||| ||||| ||||| || ||||||||||| ||||| || |||||||| |
gtttgtgcctttttct-cttctgtaattgttttgcattggacactaaaggatatagtcgatggta-acttaaagtggtctcttttttggtgtgtttattaattgcgtagGTTCATTTCCTATACAAAGGGACATTGAGAGTATTACTGGTTCTGCTTCATGATTTCCCAGAGTTCCTATGTGATTATCATTTTACTTTCTGTGATGTGA

upper sequence: GLYMA03G27260.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv00s0144g00010.t01 (Vitis vinifera), 3'ss of exon 17
-----gtttgtctatatctcggcctcaattatttgcttccaactgggtctatgcacaataatgcttctta---catctacatttgtttttttttttgtacttttttatgaccagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCATGACTTCCCGGAGTTTCTCTGTGATTATCACTTTACCTTTTGTGATGTTA
      ||  ||    | | ||  | |||||||||  |   |     |  |   |  ||| |  ||  |      ||||   ||  || ||| |||  | |||||||    ||| | | | | || ||||||||||| || ||||| ||  | ||||| || ||||| ||||||||||| || ||||||||||| || | ||| |||||||| |
gtttgcttcttcagcttattgggtttaattatttgtcttttaaatatttcagagaatatattatttgctggcttttctatccttaattgtttgtttcaattttttta----cagATACTTTTTCTATATAAAGGCACTCTAAGGGTACTGCTTGTGCTGCTCCATGATTTCCCGGAGTTCCTGTGTGATTATCATTTCAGCTTCTGTGATGTGA

upper sequence: GLYMA03G27260.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv15s0021g02610.t01 (Vitis vinifera), 3'ss of exon 13
gtttgtctat----atctcggcctcaattatttgcttccaactgggtctatgcacaataatgcttcttacatctacatttgtttttttttt-tgtacttttttatgaccagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCATGACTTCCCGGAGTTTCTCTGTGATTATCACTTTACCTTTTGTGATGTTA
||||| || |    ||  | || |||  |  |||||| || ||   | || ||  ||      || ||||||     ||||||||  |||  |||  ||||    |  ||||||| | | || |||| |||||||||||||||||| ||| ||||||||||||| |||||||||||||| ||||  ||||| |||||||| |||||||| |
gtttgcctcttttaattgcagcatcatcttcttgcttgcagctcactataggctgaaa-----ttattacat-----tttgttttcctttcgtgtttttttgaccgtgcagGTTCATTTTCTGTATAGAGGCACACTTAGGGTGCTGTTAATGCTACTTCATGATTTCCCGGAGTTTCTATGTGGCTATCATTTTACCTTCTGTGATGTGA

upper sequence: GLYMA03G27260.1 (Glycine max), 3'ss of exon 29
lower sequence: PP1S41_25V6.1 (Physcomitrella patens), 3'ss of exon 43
--gtttgtctatatctcggcctcaattatttgcttccaactgggtctatgcacaataatgcttcttacatctacatttgtttttttttttgtacttttttatgaccagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCATGACTTCCCGGAGTTTCTCTGTGATTATCACTTTACCTTTTGTGATGTTA
       |  |||| |    ||     ||||| |      |  ||  |||   || |||| |      || |  | || | | ||  | ||||   |    |   |||||||| || || || || |||||  |  | || ||  | |||||||| || ||||||||||||||| | |||||| ||||||| | ||||||||| || |
caaagcatacatatttt---ctagcgcatttggtgtacgattagtgaatgt-taagaatgat----gtattttaaattatatattgatctgtaacctgggtttggcagGTTCGGGTGCTTTACAAGGGCACGTTGCGTGTTCTTCTTGTGCTACTCCACGACTTCCCGGAGTTTTTATGTGATCATCACTTCAGCTTTTGTGACGTCA

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|193439276|gb|FK409021.1|FK409021
EST:     TGTTCCAATTTATGGAGCCTTTTCTGAGGCATGCTGAACTTGGAGAACCG                         GTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCAT
genomic: TGTTCCAATTTATGGAGCCTTTTCTGAGGCATGCTGAACTAGGAGAACCGgtttgtctat ... ttatgaccagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatgcttcttacatctacatttgtttttttttttgtacttttttatgaccagGTTCGTGTCCTCTATAAAGGCACACTTAGGGTGCTCTTAGTGCTACTTCATGACTTCCCGGAGTTTCTCTGTGATTATCACTTTACCTTTTGTGATGTTA
        ttcttac  putative branch site (score: 2)
                    catttgtttttttttt  putative PPT
               atctacatttgttttt  TA-rich tract