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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag

Basic information

species Vitis vinifera
transcript Vv18s0001g10820.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA13G29660.1 (Glycine max), 5'ss of exon 1
GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgc-tttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag
|| || ||  | ||||||||||| || ||||| || ||||| || || || |||||||| ||||| ||||| |||||||||||||| ||||| || ||||||||  ||   | |      |   |||||    |||         |  |    ||||| |  ||| |  |          |  |||||   |                                            
GGTGGAGCGCTAGGGCACCCTCCCCCAGATTCCCCAACTCTCGATTCCTCCGAGCAGGTCTACATCTCCTCACTCGCTCTCCTCAAGATGCTTAAGCACGgtaa-gtccaaaagttc---ccgtttttaacctaatcgagtcatggagtacccgatttctaaattagggttttcgtgtttctgtaattgcag--------------------------------------------

upper sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA15G09410.1 (Glycine max), 5'ss of exon 1
GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag
|| || ||  | ||||||||||| || ||||| || ||||| || || || |||||||| ||||| ||||| |||||||||||||| ||||| || ||||||||  ||           | ||||||     |  ||||  | ||  |    || |  |    |  |  |  || ||||     |||||||||||    ||| | |  ||                         
GGTGGAGCTCTAGGGCACCCTCCCCCAGATTCCCCAACTCTCGATTCCTCCGAGCAGGTCTACATCTCCTCACTCGCTCTCCTCAAGATGCTGAAGCACGgtaaagtcc----------aaaagtttc----cgttttttagcctaatc---gagtcatggggtacc--cgattacaaa-----attagggttttcgtgtttttgtaattgcag---------------------

upper sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA17G36230.1 (Glycine max), 5'ss of exon 1
-GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag
 || || ||  |||| || || || |||||||| || || || || || || |||||||| ||||| ||||| ||||| || ||||||||||||||||||||||          || |  | || | ||||||              |||   |||    || ||||  |||||| |  |   |  ||    || ||||  || |  | ||   |        ||| |  ||    
AGGTGGAGCGCTGGGTCATCCCCCACCGGATTCTCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACggta---------tgctattagaattcttatttt-----------ctcttctcgatccccttcttcgtttcactttcccatgtttttttta-ttgttcatcttataattttgaaaaccctaatttgtgtgta----

upper sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G08940.1 (Glycine max), 5'ss of exon 1
GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag
|| || ||  |||| || || || |||||||| || || || || || || |||||||| ||||| ||||| ||||| || ||||||||||||||||||||||         ||| |  | || | || |||    ||   |    |||      |    | ||| | |   ||        |   |     |||||||     |   || ||  | |                 
GGTGGAGCGCTGGGCCATCCCCCACCGGATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgta---------cgctattagaattcttcttttctcttctcgatcccttcactggtccacttttc-ctttgtttttgt-ttttgtctgataattttcaaaaccctaatttctgtgtag-----------------

upper sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 1
GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag
|| ||  |    ||    || |  || ||||| ||     | || ||||||||||| || |||||||||||||| || || ||||||||||||||||| ||||       |  ||       | |  || |   ||   ||| | | ||||| |||||| | | |  ||  |   | |||     ||  |    |||||||  | |||||   | ||||                
GGCGGTTCTGGAGGTGGACCGCATCCAGATTCACCCCTCGTTGATTCGTCGGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgta------cgctgct----tgaatcataat---ataccaggaccgttttgtcatttttatgtcca-attgcaggcgaacttc--ttgtgcgaattcaattattgttctt---acttgg----------------

upper sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ37436 (Selaginella moellendorffii), 5'ss of exon 1
GGAGGGGCATTGGGGCAC-CCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag
 | |||     | ||||  ||||  || ||||||||     | ||| |||| |||||||| ||||| ||||| || || || |||||||||||||| ||||||||      |  |  |           ||||   |  ||| |   ||||| | || |||                                                                           
-GCGGGCGGCGGTGGCATGCCTCACCCCGATTCGCCCCTCGTCGACACGTCCGAGCAGGTCTACATCTCCTCGCTAGCGCTGCTCAAAATGCTCAAGCACGgtaa------ggagggagagagctccgcattttcgtgctagag---ctttgcgcttctttcgcag----------------------------------------------------------------------

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|161715964|gb|FC067142.1|FC067142
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|71875919|gb|DT024974.1|DT024974
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|110700849|gb|EE077863.1|EE077863
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|110731528|gb|EE106018.1|EE106018
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGTTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|26261606|gb|CA812669.1|CA812669
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|161707958|gb|FC057779.1|FC057779
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|351048672|gb|FQ448946.1|FQ448946
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|161707390|gb|FC055194.1|FC055194
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|110364691|gb|EC928133.1|EC928133
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|161714686|gb|FC062666.1|FC062666
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|349809860|gb|FQ398485.1|FQ398485
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|110397855|gb|EC963800.1|EC963800
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|351044771|gb|FQ449025.1|FQ449025
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|30302146|gb|CB978940.1|CB978940
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|349811487|gb|FQ409483.1|FQ409483
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCCAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|46917963|gb|CN547292.1|CN547292
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|351041787|gb|FQ455997.1|FQ455997
EST:     GGAGCGGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|351052596|gb|FQ456444.1|FQ456444
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|294966821|gb|GW837840.1|GW837840
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGTTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|26262771|gb|CA813834.1|CA813834
EST:     TACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: TACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|37185413|gb|CF604766.1|CF604766
EST:     GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
EST: gi|351041956|gb|FQ456166.1|FQ456166
EST:     GGAGCGGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACG                         GGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG
genomic: GGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatctt ... ggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC