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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcatttgaactttgccaaactctcccctctgaacattacttgacatggattagtttgttttgctttctgtaatgcaccttctcttttgtatttgctgagacagattagcttattgactgcatattcaagatctgtctagatcgtttttaactatttgtatgacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT

Basic information

species Vitis vinifera
transcript Vv01s0011g04370.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 5
gtaatgcatttgaactttgccaaactctcccctctgaacattacttgacatggattagtttgttttgctttctgtaatgcaccttctcttttgtatttgctgagacagattagcttattgactgcatattcaagatctgtctagatcgtttttaactatttgtatgacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT
                                                                         ||||||||  ||  |||||| ||         ||||    |||| ||  || | ||| ||    ||  || ||  |  ||   ||||||||    | | ||||| | ||||||||||| |||||  ||||||||||||| ||||| |||||  |||| |  ||||||||||| |||||||||
-------------------------------------------------------------------------gtaatgcat-ttaacttttggat---------caga----cttactg-ttgtagatttaatgcttga-taaatgctaatttgatatttgtact-ttgagcagAATTACCTGAAAGATCATATGGAACTGATTGCCGCATATATGTACCTGACCATCCGAAAAGCAGGTTTAACAATGTTTAT

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 5
gtaatgcatttgaactttgccaaactctcccctctgaacattacttgacatggattagtttgttttgctttctgtaatgcaccttctcttttgtatttgctgagacagattagcttattgactgcatattcaagatctgtctagatcgtttttaactatttgtatgacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT
                                                                                        |  || ||||        |     ||||| ||  || | ||| ||    ||  || ||  |  ||   ||||| ||    | | ||||| | ||||||||||| |||||  ||||||| ||||| ||||| |||||  ||||||  ||||||||||| |||||||||
---------------------------------------------------------------------------------------gtaatgcatttagctttctaatcaggcttagtgg-tgtagatttaatgcttga-taaatactaatttgatatttctact-ttgagcagAATTGCCTGAAAGATCTTATGGAACTGATTGTCGCATATATGTCCCTGATCATCCAAAAAGCAGGTTTAACAATGTTTAT

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 6
gtaatgcatttgaactttgccaaactctcccctctgaacattacttgacatggattagtttgttttgctttctgtaatgcaccttctcttttgtatttgctgagaca--gattagcttattgactgcatattcaagatctgtctagatcgtttttaactatttgtatgacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT
||||| || |   | | |       | |   |||||||  ||  ||   ||  |||  ||   | |      |||| |  |  ||        | |||| | || ||  ||| |   | ||  || ||  || || || |||        ||| ||  | ||||     |||  |||||||||| |||||||| ||||| ||||| || || || ||| |||||||||| ||  | |||||||||||||||||||||
gtaattcaatccgattctttt---ttattagctctgaa--ttggttagaattaattgattatgtatcagcgttgtatttgagatttgaaaacatttttggttagtcaaggataaagctgttttcttcagtttaaaaatatgta------atttcta--tgtttg---atcttggcagAACTTCCAGAAAGATCTTATGGCGCTGACTGTCGTATATATCTGCCTGAAAACCCTGCAAGCAGGTTTAAGAATGTTTAT

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 8
gtaatgcatttgaactttgccaaactctcccctctgaacattacttgacatggattagtttgttttgctttctgtaatgcaccttctcttttgtatttgctgagacagattagcttattgactgcat---attcaagatctgtctagatcgtttttaactatt-tgtatga-cttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT
                                                       || ||   | || ||  | |     | |||    || |       ||  |   |||   |   |  ||||||   |||  |||| ||   | ||  ||  ||| || | ||| ||| |||  |||||||||| || ||||| ||||| ||||| || || || ||| |||||||||| ||  | |||||||||||||||||||||
------------------------------------------------------gtaattcaatctgattcttttttattagctttgaattggctggaaatggaattaattgattatgtatctgcattgtatttgagatttgaaaacatttttggtaattactatgtttgatcttggcagAACTTCCAGAGAGATCTTATGGCGCTGACTGTCGTATATATCTGCCTGAAAACCCTGCAAGCAGGTTTAAGAATGTTTAT

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgcatttgaactttgccaaactctcccctctgaacattacttgacatggattagtttgttttgctttctgtaatgcaccttctcttttgtatttgctgagacagat-tagcttattgactgcatattcaagatctgtc-tagatcgtttttaactatttgtatgacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT
                                                                                          |   | || | ||||   ||   | |||||    |    | | | |||  |  | || | | ||      ||||  | |  |  ||||||||||||| | ||| || |||||||||||||| || |||||||||||  | ||||| | ||||||||||||| |||||
-----------------------------------------------------------------------------------------gtaagagtttcggagaggaatgctgtttattcgaggagc-taccacatcaatgattgaccatcttattgagtttgc-tcatgttgcagAACTTCCTGAGAAATCATACGGTGCTGATTGCCGTATATATGTGCCTGATCACCCAACAAACAGGTTTAAGAATCTTTAT

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|349828936|gb|FQ419269.1|FQ419269
EST:     TGATGATGCTCGGCAATTCATGAAGTTTCTCCATCCTGATCTTGGTGTTG                         AACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAA
genomic: TGATGATGCTCGGCAATTCATGAAGTTTCTCCATCCTGATCTTGGTGTTGgtaatgcatt ... gacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAA
EST: gi|351026887|gb|FQ436540.1|FQ436540
EST:     TGATGCTCAGG-AATTCATGAAGTTTTCTCCATCCTGATCTTGGTGTTTG                         AACTTCCTGAAAGATGGAATGGTGCAGATTGCCACATTTA
genomic: TGATGCTC-GGCAATTCATGAAGTTT-CTCCATCCTGATCTTGGTGTT-Ggtaatgcatt ... gacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcatattcaagatctgtctagatcgtttttaactatttgtatgacttaacagAACTTCCTGAAAGATCGTATGGTGCTGATTGCCGCATTTATGTGCCTGAAAATCCAACCAGCAGGTTTAAGAATGTTTAT
                             ttttaac  putative branch site (score: 2)
                            tttttaactatttgta  TA-rich tract