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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattctgacacaacttttgccag

Basic information

species Vitis vinifera
transcript Vv06s0061g01120.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttc-----tctatcattcctcctttgttcttttgaggt------tgg--------agtaaaattctgacacaacttttgccag
| ||| |   | || || || || ||  | ||||||||||| ||||||||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||||||    |||| |||      || | ||  ||   |||| ||  |  |||      |||        |   ||||  |||  ||||| || | ||
GAACCTATGATTGACGTGAGTTCGAAGCAGTTCTATGGTGAAGGATATGATGATAGTGATAAGAGGATTCCTGACATGACCATAATCAACAAGCAGCTTGgtatt-tactgtcttcaataacctgttatgtctatgttgtactagttgggtaaccagtggttcataataaccaaatattgattcaactgtt-ctag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 6
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtat--cgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattctgacacaacttttgccag
|  || |   | || || || || |   | ||||| ||||| ||||| ||||||||||| ||||||||||| |||||||| |||||||| || || || |||||   |  |    |  ||| |   |   |  ||||| |    |  |    || | || |  ||   | || ||    
GAGCCTATGATCGACGTGAGTTCGAGTCAGTTCTACGGTGAAGGATACGATGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtgcatggtggtctgtgggtatgc--ttgttttccctaactaatggtcagatgcctactgga-ttatgtag-

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA12G30490.1 (Glycine max), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttctctatcattcctcct-ttgttcttttgaggttggagtaaaattctgacacaacttttgccag----------------------------------------------------
  ||| ||| | ||||| |||||||||||||| |||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||  || ||||||||    |  | ||||     |    |    || ||    ||||    |     ||| ||||||||   |||   |                                                     
AAACCTACTATTGATGTGAGCTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGAGAATTCCTGACATGACCATAATTAATAGGCAGCTTGgtatgtttccttgttctactctacctttgagattattaaaatgagaaatgctaggaatactgacacagtcttttgaacaaactcctcttaaaataatttacctgttaatggggtgttacttctttatcag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 6
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtat-cgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaa-attctgacacaacttttgccag
  ||| ||| | ||||| || ||||||||||| |||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||  || ||||||||    |||  |||  || |   |     ||| ||    | |  |    || ||     |   ||  |||||  |||
AAACCTACTATTGATGTGAGTTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGAGAATTCCTGACATGACCATAATTAATAGGCAGCTTGgtatgtttccttgttttactttacctttaagtttattaaaataatctaactgttaacggggtattacttcttttatcag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgta---tcgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattctgacacaacttttgccag-------------
  ||| ||  | ||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| || |||||||||||||| || || || |||||||   |  | | ||  |   | | |  ||   ||||  |  || || ||| |    | || |      | |  |    |             
ACACCTACCATTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGACAGTGACAAGAGAATCCCTGACATGACCATAATAAACAAGCAGCTTGgtaggtttactcagtcgttaatttaa--ccatatttgaccccttaagattgtaacttacttttcttgttaatggtcattgcttctcctctcag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgta--tcgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattct----------gacacaacttttgccag
  ||| || || ||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| || |||||||||||||| || |  || |||||||  |  ||    | | |   | |  | |  ||    ||||| || ||| |    ||||            | ||   ||| |  |||
ACACCTACCGTTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGAGAATCCCTGACATGACCATAATAAACAGGCAGCTTGgtaggtttcctcactctttaatttaaccatatttgacccttttaagattgtaacttaatttacctgttaatggtcattgcttctctcag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaa-----attctgacacaacttttgccag---------
   ||||| || ||||| ||||||||||| || || || || || ||||||||||||||||||||||| |||||||||||||| || ||    ||||| ||||   |    |  || | | |||      |    |  ||| |  |   | | ||     ||||||| | || ||| | |           
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttctc-tatcattcctccttt------gttcttttgaggttggagtaaa-attctgacaca-acttttgccag
   |||||  | || || ||||||||||| || ||||| || || ||||||||||| ||||||||||| |||||||||||||| |||||    |||||||||| |  ||| ||||||  | | |||  || |||      ||     ||   ||  | |||| | ||||      ||  |    ||
AGTCCAACGATCGACGTGAGCTCCAAAGAGTTTTATGGAGAAGGTTATGATGACAGCGACAAGAGAATCCCAGACATGACCATCATCAACCGTCAACTTGgtaacttcctcttttcttgtctgattagtcttttctaacagtcacaatgtttttctaataaatactctggtgtggacaataattag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ07025 (Selaginella moellendorffii), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatc-gccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattctgacacaacttttgccag---------
|  || ||  | || || ||||| || || || || || |||||||| |||||||| |||||| | |||||||||||||| || ||||| || ||||| ||||   ||   | |     | |   |  |  | | |         ||      | |  |||  | |   |||||             
GAGCCCACAATCGACGTGAGCTCGAAGGAGTTTTACGGGGAGGGATACGATGACAGCGACAAGCGCATTCCAGACATGACGATCATCAAGAAGCAACTGGgtaagagctacgatcgtgttctagcttttgttctatcaaccaatcgtgtctaaacatctctctctctctttttggtgtttgatccag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ18978 (Selaginella moellendorffii), 5'ss of exon 8
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatc-gccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattctgacacaacttttgccag---------
|  || ||  | || || ||||| || || || || || ||||||||||||||||| |||||| | |||||||||||||| || ||||| || ||||| ||||   ||   | |     | |   |  |  | | |         ||      | |  |||  | |   |||||             
GAGCCCACAATCGACGTGAGCTCGAAGGAGTTTTACGGGGAGGGATATGATGACAGCGACAAGCGCATTCCAGACATGACGATCATCAAGAAGCAACTGGgtaagagctacgatcgtgttctagcttttgttctatcaaccaatcgtgtctaaacatctctctctctctttttggtgtttgatccag

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|71872790|gb|DT021845.1|DT021845
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|33402337|gb|CF207964.1|CF207964
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|110405386|gb|EC970927.1|EC970927
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|37187794|gb|CF607147.1|CF607147
EST:     ACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: ACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|30298239|gb|CB975033.1|CB975033
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|33402259|gb|CF207886.1|CF207886
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTC-GATCNTTTGCTTGAGTCAACCCTCACC
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGA-TTTGCTTGAGTCAACCCTCACC
EST: gi|349828491|gb|FQ417233.1|FQ417233
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|22007527|gb|BQ792561.1|BQ792561
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|33404942|gb|CF210569.1|CF210569
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|110397475|gb|EC963215.1|EC963215
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|110420047|gb|EC986308.1|EC986308
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|110396028|gb|EC961702.1|EC961702
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|110371215|gb|EC935056.1|EC935056
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
EST: gi|71888796|gb|DT037851.1|DT037851
EST:     TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTG
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTG
EST: gi|45771342|gb|CN007194.1|CN007194
EST:     TGACAGTGACAAGAGAATCCCAGACATGACCATAATCAATAAACAACTTG                         GTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT
genomic: TGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccct ... cttttgccagGTTGGAACCCTAAGACATCGCTCTGGGATTTGCTTGAGTCAACCCTCACCT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaaattctgacacaacttttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA