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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA

Basic information

species Glycine max
transcript GLYMA09G18450.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27040.1 (Oryza sativa), 3'ss of exon 4
--gtacttttctgtcttttagaaacttttcctaaccttat-tttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
   |||  | || || |||  | |  | |  | |  |||  | |     |||   ||  |     |||  ||   ||     |  |  | | ||||  || ||| ||| ||||| || ||||| ||||| || ||||| || || ||||||||||| || || |||||||||||||| |||||||||||||||||
gtatacgatgctctcatttgtagatatctattgaagttacatctttggttcatgctga-accatataatttaaccat-----agagtttgtgcagGGATTCTATATTCGGTACTTATAACTGCTGTGATTACTGATGCAATTAAGGATGGTGTTGGTCGTCCTCGCCCAGATTTCTTTTGGCGTTGTTTCCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27030.2 (Oryza sativa), 3'ss of exon 3
--gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
   ||   | || || | |  | |  | |   ||    |||   | | |||||||  | |||   |  ||  | | ||   | |   ||  ||||  || ||| ||| || || || ||||| ||||| || ||||| || ||  |||||||||| || ||||||||||||||||| |||||||||||||||||
gtatatggtactctcatatgtagatatctatcaa----attacactt-tcacttt--tttagttcatgct--gaactggacactttgta--cagGGATTCTATATTCGGTGCTTATAACTGCTGTGATTACTGATGCAATTAAGAATGGTGTTGGTCGCCCACGCCCAGATTTCTTTTGGCGTTGTTTCCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 3
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatatt--cagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
          || ||||| | | | ||  |      |||  |   || |  |   || |    ||   |||  ||| ||  |   | ||   |||  |  |||  ||||| || || |||||||| || || ||||| || || |||||||| || || |||||||||||||| |||||||| |||||||| ||
----------gtattttacatattcttgatcctaccattaagttgataatataaataaaaaggaata-atgc-ttgacattttttttttggtagGGATCCTATACTCTGTGCTTATAACTGCGGTAATCACAGATGCAATTAAGGATGGTGTGGGTCGTCCACGCCCAGATTTTTTCTGGCGCTGTTTCCCAGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
gtacttttctgtcttttagaaact-tttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
||    |  |||  |||  |  || |||  |     || | | || ||   ||||  ||  | || |  |    | ||  |||||   | |||| ||  ||||||| || || || || ||||| ||||| ||||| || |||||||| ||||| || || || ||||||||||| ||||| ||||| |||||
gtgagctcatgttctttctattctgttttgttttgctagtctacacat---tttgtaatttcttatctgaaacctagc--aatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G024615_T05 (Zea mays), 3'ss of exon 4
gtacttttc-tgtcttttagaaacttttcctaaccttattttgcatatca-----ctttgctatagcctaacctatgtat-tgccaaatgcatattc---agGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
||| ||| | | | | ||   |    |||    | ||  || | | |  |     | |  | |   |   |   | |||| ||  ||||| | |||    |||  || |||  || || ||||| ||||| ||||| || ||||| || || ||||||||||||||||| || |||||||| |||||||| |||||||||||
gtagtttacatatttattgtgattccttcgattcattgattagtacaagagaaaacatatccagtacaagaaaaacgtatctgaaaaatggaaattttgtagGGATTCTATACTCAGTGCTCATAACTGCAGTGATTACTGATGCAATTAAGGATGGTGTTGGACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgcta-tagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
                || |  |  || ||  ||  |||    ||   |||||   | ||        | || | |   |  ||      |||| ||  ||||||| ||||| |||||||| ||  |||| ||||| || || ||||||||||| || ||||| || ||||||||||||||||| ||||||||
---------------gtacattcactttctcgccagattcactattctactttatcaatattacttattctgaaatctaacttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G050658_T01 (Zea mays), 3'ss of exon 4
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
          || || || | | || |  |  | | | | ||   || | |     | |  |  || | || | ||  || |   ||    ||  || |||  || || || || ||||| ||||| || ||||| || || ||||||||||||||||| || |||||||| |||||||| ||||||||| |
----------gtattatacatatttatgatcccttcaatatgttgattagtacaagagaaac--acatctgaaatggaaattttgta----gGGATTCTATACTCAGTGCTGATAACTGCAGTGATTACTGATGCAATTAAGGATGGTGTTGGACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G447433_T08 (Zea mays), 3'ss of exon 5
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
                ||       |||  |||   || ||   | ||| ||  |  |    |||  |||||    |  ||   ||||  |||  | || | ||| || || || ||||| ||||| || ||||| || || ||||||||||| || || || ||||||||||| ||||||||||| |||||
---------------gtacctgacattctaaac---atgttatttgtcaattgacagt--tttaatttatgttgaacttaaaaaatatgtagGTATCTTGTATTCAGTGCTTATAACTGCTGTGATCACTGATGCAATTAAGGATGGTGTTGGTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
|||| | | | |  ||   |   | || |     |    ||   | |  ||   ||  |   | |  | |||  |      | | | |||||| ||||| || |||||||| || || |  || ||||| |||||||| || || | |||||| || || || || |||||||| |||||||||||||||||
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagct---cttgattttgaggtgtgttctcttgggt-cttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA

upper sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 3'ss of exon 2
gtact-tttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
|||    || |  | ||   | | || |   |  |   |  ||  | |  | |||   |    |     ||| |||      ||||| || ||||||| |||| |||||||| || || || || ||||| ||||| || ||||||| |||||| || || || ||||| ||||| ||||||||||||||| |
gtatcactttttcccttcctagatttctttgagtcaggtactgt-tgtttccttgtggtgcattgcttaatggattat-gtgtgcatgtttagGCCTTCTATTCTCTGTACTGATCACGGCAGTTATAACTGATGCAATTAAAGATGCTGTTGGCCGACCTCGTCCAGACTTCTTTTGGCGTTGTTTCCCTAA

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|298198112|gb|HO039651.1|HO039651
EST:     TTACTATCTCATCCGAAAGGATGTTTATGACTTCCACCATGCTATCTTCG                         GCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAG
genomic: TTACTATCTCATCCGAAAGGATGTTTATGACTTCCACCATGCTATCTTGGgtacttttct ... gcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
                      gcctaac  putative branch site (score: 2)
                              tatgtatt  TA-rich tract