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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgctgcgtatatatatggcagtattgatttgatggagatcactaatcaggatacgtgaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG

Basic information

species Glycine max
transcript GLYMA11G09890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 3'ss of exon 5
gtattg-ctgcgtatatatatggcagtattgatttgatggagatcactaatcaggatacgtga-aaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG
|||| | |||      | |     | | |  |  |  ||   |||   |  || |  |  ||| | | | |||| ||   |||  |||||||| | ||| |   |||||| || || || |||||||| |||||||||||||| || ||||||||||| ||||| ||  ||||  | ||||||||||
gtatagtctgtcgtcttgtcacaaaatttgaacattgtgtgcatcgg-atccatgtcagttgacataatgttctctcattaat--agGTTGGCATCAAGGACCATGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATG

upper sequence: GLYMA11G09890.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G090338_T01 (Zea mays), 3'ss of exon 5
gtatt-gctgcgtatatatatggcagtattgatttg---atggagat-cactaatcaggatacgtgaaaactt------ttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG
||||| |      |||| | ||  |   ||| ||||   ||| |||| ||   ||  |||  | ||  |  |        | | |||||     |||||||  | ||| ||   |||||||||||||| ||||||||||| ||||||||||| || ||||||||||| ||||| || |||||  | ||||||||||
gtatttgtctgacatat-tgtgagaaatttgttttgtagatgcagatgcatatatttggagccctgtcatttcatgttactgtatctgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG

upper sequence: GLYMA11G09890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g02330.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------gtattgctgcgtatat---atatggcag-tattgatttgatggagatcactaatcaggatacgtgaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG
                                 | |  ||  | || ||   |  |||||| |  | ||  | || || |  | | |    |  | | || |   |||| | ||  || |||||||| || ||||| | ||| ||||||||| |  || ||||||||||||||||||||||||| ||||| |||||||| ||||||||||| || |||||||
gtatattactggaaacacaattctattagtccagcaaagcaccctagatgagaagtggcagatgatcatcaggtgtagtttcccattgttcactcattaacaggattctctatgatat-cagGTTGGTCTCAAGTACAATGAATCTGTGGTTATTCGGGTAACTGGCTGCCCTAATGGTTGTGCGAGACCTTACATGGCCGAACTTGGACTTGTCGGTGATG

upper sequence: GLYMA11G09890.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ27223 (Selaginella moellendorffii), 3'ss of exon 4
gtattgctgcgtatatatatggcagtattgatttgatggagatcactaatcaggatacgtgaaaacttttctgtctgcaatt---cagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG
                                 ||||     |   |        |  || ||| |||| || |||   |||    |||| ||||| ||| |    || ||  |||| ||  |  | || || || |||||||||||||| || ||||||||||| ||||||||||| || || ||||
--------------------------------gtgatttgtcttgttgtgtttcttgtgttaaatctttgctctctattattgcttagGTGGGCCTCAAGGAGGCGGATTCGATGGTGGTGCGAGTCACCGGGTGTCCTAATGGTTGTGCGAGGCCATACATGGCAGAACTTGGACTGGTCGGAGATG

upper sequence: GLYMA11G09890.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ33435 (Selaginella moellendorffii), 3'ss of exon 6
gtattgctgcgtatatatatggcagtattgatttgatggagatcactaatcaggatacgtgaaaacttttctgtctgcaattc----agGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG
                                 ||||     |   |        |  || ||| |||| || |||   |||     |||| ||||| ||| |    || ||  |||| ||  |  | || || || |||||||||||||| || ||||||||||| ||||||||||| || || ||||
--------------------------------gtgatatgtcttgttgtgtttcttgtgttaaatctttgctctctattatttgcttagGTGGGCCTCAAGGAGGCGGATTCGATGGTGGTGCGAGTCACCGGGTGTCCTAATGGTTGTGCGAGGCCATACATGGCAGAACTTGGACTGGTCGGAGATG

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|46492779|gb|CN472335.1|CN472335
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|193467858|gb|FK430829.1|FK430829
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|9903367|gb|BE612335.1|BE612335
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|27809358|gb|CB063780.1|CB063780
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|120533624|gb|EH261757.1|EH261757
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|9903129|gb|BE612097.1|BE612097
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|207803162|gb|GD775285.1|GD775285
EST:     AGCGTGGGATACCTAACATTCTTAAGCGGATTCGTGCTGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|15000299|gb|BI321113.1|BI321113
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|8283363|gb|BE020924.1|BE020924
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTGTTTGATAAG                         GTTGGCCTGAAG
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAG
EST: gi|207760127|gb|GD730874.1|GD730874
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAA
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAA
EST: gi|10232272|gb|BE801160.1|BE801160
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTATTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGGTG-TTGTAAAGATAGCTGGGCTGCA
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTG-TGGTTGTAAGGATAACTGG-CTGCC
EST: gi|42722808|gb|CK768707.1|CK768707
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
EST: gi|6747403|gb|AW317859.1|AW317859
EST:     AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAG                         GTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT
genomic: AACGTGGGATACCTAACATACTTAAGCGGATTCGTGATGTTTTTGATAAGgtattgctgc ... tgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgatggagatcactaatcaggatacgtgaaaacttttctgtctgcaattcagGTTGGCCTGAAGTATAGTGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATG
             cactaat  putative branch site (score: 2)
                                   cttttctgtct  putative PPT
                               aaaactttt  TA-rich tract