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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctaaaatactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC

Basic information

species Glycine max
transcript GLYMA20G24820.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
gtatgcctaaaatactgttgtgtttagattgtttcttttca-aaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
        || || ||    | |||  |||  | ||| | | | | |    |  ||  | || | |  ||| |||   ||| |||  ||| ||  |   || | || |       |||| |||||||||||||||||  ||||||| ||||| ||||| ||||| ||| ||||||| |  || || |||||||| ||||||||||| ||||| ||||
-----ttgaacatgcttgaatatttttatttatgcttgttatatactacagtcattg-tatctacagtaaacatcc--tttttaattttttgtctt--gatattcttt-------agGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G151236_T03 (Zea mays), 3'ss of exon 7
gtatgcctaaaatactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
   | | ||| |||   | | |    |  ||| |     |   |  | |  | ||  |||    ||  || | |     | ||  | |  || | |   ||    | |      |||| |||||||||||||||||  | ||||| ||||| ||||| ||||| ||| |||||||||  ||||||||||| || |||||||| || ||||| ||||
--cttcttaatataagctcggg----ggctgtcttacccccgcaggtcgagttttttttttttaaattaacaccg----tttattactgtgtccattgcttgtaccct------agGTGAATGAGGCTAAGAATGTGCTCAAGCTATGTGATTTTGGGAATGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTTAGCCGTTTCTATC

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 8
----------------------------------------------------------------------------gtatgcctaaaatactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                                                                              || | ||||| ||| || | |  | ||  | || |||||   ||||       || | ||      |||| | ||||   | ||||||  | | || || | | | ||  | |||| |||||||||||||||||  | ||| | ||||| ||||| || || ||| |||||||||  ||||||||||| || |||||||| || ||||| ||||
gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaa-actattttttggatatgctgtcatttcattcttttacgcacaaaatgcac-----aataccaatttaacaccatttatgtgtcca-ttgcttgtatt--ctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
lower sequence: AT3G25840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcctaaaatactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                                 ||  |   |  |||  || |||   | | |    |   |     ||||||||  || | ||||  |         ||| | |||| |||||||  || ||||| || ||||||||||| ||||||||||| |||||||| || ||||| ||||||||||| |||||||| ||||| |||||  
--------------------------------gtcagtcacacttttcattggttttctcctacttaattcaatagctttctaactgttgggtctttga---------ttgtccagGTCAATGAGGGGAAAAATGTCTTAAAGCTTTGTGATTTTGGTAATGCAATGTTTGCAGGCAAAAACGAAGTTACACCGTATCTTGTTAGTCGCTTTTACA

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G13350.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcctaaaatactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                        ||   | |  ||| ||    |||| | |  |  ||       ||   |  ||  || |||| | | ||  |      ||||   ||  | |||| |||||||  |  ||    || ||||||||||||||||||| ||| ||||||||||||| ||| |||||||||||||||||||| ||||| || ||  
-----------------------gtaagctata-cttgtctgtgtttt-tctcctgctt-------gatgcacataaattttaacttctggtcgt------tccttgattatccagGTGAATGAGGGAAGAAACACGTTAAAGCTTTGTGACTTTGGTAGTGCAATGTTTGCTGGTACAAACGAAGTTACACCATATCTTGTTAGTCGCTTCTACA

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 8
gtatgcctaaa--atactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
||| |  | ||  ||||| || |||  || |||  |   || |   |||| |||||||        || |||| | |   ||  |   |    |   |  ||| |||||||     ||||||||||||| || |||||  |||| || ||||| |||||||||||||||||| |||||||||||||| ||||||||||||||||||| || |||||||
gtaggttttaagtatacttttatgtccag-ttgcctgcctt-agttttttatttgttat-------aataaat-tttgcattgaattttactatatattcattgcctctttc----agGTAAATGAGGCCAAAAATGTCCTGAAACTCTGTGATTTTGGTAATGCCATGTTTTCTGGTAAAAATGAAATTACACCATATCTTGTGAGCCGCTTTTATC

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|254316086|gb|GR825895.1|GR825895
EST:     TCCGGAACTGTGGTGTTCTTCATTGTGATATAAAGCCAGATAATATGTTG                         GTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATG
genomic: TCCGGAACTGTGGTGTTCTTCATTGTGATATAAAGCCAGATAATATGTTGgtatgcctaa ... ttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
                 ttctaac  putative branch site (score: 1)
                              ttcttcaatttcctct  putative PPT
      aaatatctattttcta  TA-rich tract