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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG

Basic information

species Glycine max
transcript GLYMA10G00830.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
                                               |   || | |    | |     | |  | || |  | |  | ||| |        | ||| |||||||||||| || ||  |||| |||||||| ||||| ||||| |||||||| || ||||| ||||| || |||   |||||  |||||
----------------------------------------------gtaagcatctccttgcaccatcgatcgcattgatg-agtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtt-tcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
            ||   | |      ||||||      ||||     ||           |  || | |||   | |||| || ||  ||| |   |   | ||  | | |  |||||||| || || || || |||||||||||||||||||||| ||| || |||||||||||||| ||||||   ||||||||||||
------------gtaggtgcagcaaatctgtt----gggtcttgttctgttttgtttcttcaactca-aaatacattgttgtcgata-attttttcgggttttc--ttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctga-tgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
                             ||     ||| |  || ||  | |    |   |  | ||    ||  |||    |   | | ||  ||     ||      |  ||||||||||| || || || |||||||||||||||||||||| ||| |||||||||||||| || ||||||   |||||||| |||
-----------------------------gtaggtgaagccaacctattcctatttgtggtctttgatttctttggtgtaaataaataatatgggtgaataatcttgagatttagGTGGTCTCTTGGCGCCATTATGTATGAAATGCTTGTGGGGTTTCCGCCCTTTTATTCAGATGACCCAATGACAACTTGTAGGAAG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 6
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggcc---acccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
                        ||  |  |  |||| | ||  |||   |      |      ||  ||  | ||| | |    ||  |  |   ||||   | |||   |||||||||||||| || ||||| ||||| |||||||||||||| ||||| || ||||||||||| ||||| |||   |||||||| |||
-----------------------gttggttctctaaaactgtcatcatcttctatgatctgttttccccatgga-ttagtttcctcatataaccatctgtt---tgaatttctccagGTGGTCTCTTGGTGCTATCATGTACGAAATGCTTGTGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
                                                              | ||    | | ||  | || |  |    ||||  ||  | |  |   | ||||||||||| |||||||||||||| || ||||| || |||||||| ||||| ||||| |||||||| ||||  |||||  | |||
------------------------------------------------------gtaagaggcatttctgattgaaaatatctac-cggcttgat--tgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
                                               |      | || |          | | ||  | || |  |    ||||  ||  | |  |   | ||||||||||| |||||||||||||| || ||||| || |||||||| ||||| ||||| |||||||| ||||  |||||  | |||
----------------------------------------------gtaagaggcacttct--------gattgaaaatatctac-cggcttgat--tgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

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|254348922|gb|GR852601.1|GR852601
EST:     ATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG                         GTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTT
genomic: ATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTGgtaatataga ... atgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG
                             ttctgat  putative branch site (score: 3)
                                              tgcttcc  putative PPT
     ttataaacttaatgtt  TA-rich tract