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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtcccctctccttttttttttcttcttgttttgctctctttatcaaatcttatttttcctttaatctaattcgcggttctctatattttcaataacaataagttgaatcctttgaggaattgatatgtcaagaaattcttcctttctaattctaaattgattttgctgacagatgtttcttgtgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGCCCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGA

Basic information

species Glycine max
transcript GLYMA20G16100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G42050.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgtgtcccctctccttttttttttcttcttgttttgctctctttatcaaatcttatttttcctttaatctaattcgcggttctctatattttcaataacaataagttgaatcctttgaggaattgatatgtcaagaaattcttcctttctaattctaaattgattttgctgacagatgtttcttgtgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGCCCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGA
                                                                                                ||   || |     ||| ||      | || |  |       ||| || |||  |  || | | |||    ||  ||  ||  ||  ||         |||  |||| ||| ||||||| || || || ||| | |||||||||||  | ||  | ||||| ||||||||||||||||||||||| ||||| ||||  ||
-----------------------------------------------------------------------------------------------gtattcatca-ccacatctttcttcttactgtttcg-------attgtttcttcttggttttgatttg----tggggatggaaattgttt---------agGATTGCCACCAAGATACAGGGACTCGGTTAGAGCGATAACTCCAGGACTTCCTCTGTTTCTTTACAACTACTCCACTCACCAACTTCATGGAATCTACGA
















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|192309118|gb|FG999065.1|FG999065
EST:     TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
EST: gi|14205657|gb|BG839335.1|BG839335
EST:     TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCA-GGMTGC
genomic: TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
EST: gi|192313456|gb|FK005522.1|FK005522
EST:     GATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCCCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
genomic: GATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
EST: gi|58019242|gb|CX705984.1|CX705984
EST:     TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
EST: gi|58018944|gb|CX705686.1|CX705686
EST:     TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
EST: gi|21602164|gb|BQ612495.1|BQ612495
EST:     TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
EST: gi|254346210|gb|GR859823.1|GR859823
EST:     TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccc ... tgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcctttctaattctaaattgattttgctgacagatgtttcttgtgctttgtagGTCTGCCTCCACGATACAGAGATTCAGTAAGAACAATAACTCCAGGGTTGCCCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGA
                          tgctgac  putative branch site (score: 2)
                                      tttcttgt  putative PPT
     tttctaattctaaatt  TA-rich tract