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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaactccaaactgttacatagggaatgtgttgtgtgcaccagatcttttttactcctctttattggtttgattattttttactcctctttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGTTGCAGTCTTTGCTGAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07240.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 18
--------------------gtagaaactcca-aactgttacatagggaatgtgttgt---gtgcaccagatcttttttactcct---ctttattggtttgattattttttactcctctttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGTTGCAGTCTTTGCTGAG
                     |      |||   | || ||| ||   ||| || |      ||  || | |  || ||     |    ||| |    |  |||  |    |||  |  | | || ||| || ||||| |||||| | || |||||||||||||||||| ||||||| |||||||| ||||| |||
gtagaattctgatccagaacatgtgttttccttgattgctacttacctaatatgcttcctcttgttcctgttgcttattgagtttaaaatttgtcatatgtattgatacacacttgtgatcaatttcagATCGGATAGAGAACTTATAGGTCCCAACAATCAATATCTTTCCAAAATTGTTGCAGTTTTTGCCGAG

upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 18
-----gtagaaactccaaac-tgttacatagggaatgtgttgtgtgc---accagatcttttttactcctctt---tattggtttgattattt----------------tttactcctctttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGTTGCAGTCTTTGCTGAG
     ||    |  || ||| ||||   |     || |||| | | |   | | | |   | ||  |||| ||   | |||  || | ||||                    ||| |  || | || ||| || ||||| |||||| | || |||||||||||||||||| ||||||| |||||||| ||||| |||
gtagggttatgatcccgaacatgtttttttttttat-tgttatttacctaatctgcttcctcttgttcctgttgcttgttgacttcaatattcggcatatgtattgatacacacttccattcaatttcagATCTGATAGAGAACTTATAGGTCCCAACAATCAATATCTTTCCAAAATTGTTGCAGTTTTTGCCGAG
















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|34546248|gb|CF514480.1|CF514480
EST:     TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAG                         GTCAGATAGGGAACTTTTGGGGCCCGACAATCAATATCTTCCCAAAATAGT
genomic: TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAGgtagaaactc ... ttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT
EST: gi|352769684|gb|FQ468612.1|FQ468612
EST:     TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAG                         GTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT
genomic: TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAGgtagaaactc ... ttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT
EST: gi|32246132|gb|CD711951.1|CD711951
EST:     TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAG                         GTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT
genomic: TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAGgtagaaactc ... ttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT
EST: gi|161718955|gb|FC065096.1|FC065096
EST:     TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAG                         GTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT
genomic: TTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAGgtagaaactc ... ttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttactcctctttattggtttgattattttttactcctctttatttacagGTCAGATAGGGAACTTTTGGGGCCCAACAATCAATATCTTCCCAAAATAGTTGCAGTCTTTGCTGAG
                      gtttgat  putative branch site (score: 5)
                            ttattttttactcctc  CT-rich tract
               tttattggtttgatta  TA-rich tract