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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaaaactggcacatttgaattattttgccttctcctgaaagttcatgatccacttaactcgtctcatgaatgtgcaattggta...

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA14G37520.1 (Glycine max), 5'ss of exon 33
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaaaactggcacatttgaattattttgccttctcctgaaagttca---tgatccacttaactcgtctcatgaatgtgcaattggta----
|| || ||||| || ||||||||||| ||| ||||||||||||||||||||||  || | ||||||||||  |||  | | ||       |||  | |   ||  | || |  ||   |||||| |     |||| ||  |  || ||    |  |||   ||    ||    
GCTGTTTTGAGGGCATTATATGCTTATTTTACTGACAGGCCTTTGAAAGAAATTGCAGATATTGAGgtaatatattcatattt-------ggctgaatgtgatgttcttactctcgtatgaaagatggagttgatgcaaatgcctagttgtgttcatggcaaacatttaagaa

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 22
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaa-aactggcacatttgaattattttgccttctcctgaaagttcatgatc-cacttaactcgtctcatgaatgtgcaattggta-
|| || ||||| || ||||||||||| ||| ||||||||||||||||||||||  || | ||||||||||  |||    | |||    |  |  |  ||   | | |  ||  |    |    |||| ||||     | ||| |    |||||       | || | | 
GCAGTTTTGAGGGCATTATATGCTTATTTTACTGACAGGCCTTTGAAAGAAATTGCAGATATTGAGgtaatatattcgtatttagctgagcgtgatgttcttactctcgtg--tgaaacatggagttgatgaaaatgcctaattgagttcatgg-caaatatttaggaa

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 24
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaa--aactggcacatttgaattattttgccttctcctgaaagttca--tgatccacttaactcgtctcatgaatgtgcaattggta
 | || ||||| ||  |||||||||| |||||||||||||||||||| ||||| || || || |||||||  | || |   || |    |    |   ||   | ||  | |     |  | ||  |  |  |||| |  ||  |     | |      ||||| |    
-CAGTTTTGAGGGCACTATATGCTTATTTTGCTGACAGGCCTTTGAACGAAATTCCGCATATAGAGGtaatttgtgaattatttagctgaacttcttgttcttactagatgggtgcatattaaacatggagttgatgc-tttggcctaattgacttggttgcaaatat--

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 23
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaa--aactggcacatttgaattattttgccttctcctgaaagttca--tgatccacttaactcgtctcatgaatgtgcaattggta
|| || ||||| ||  |||||||||| ||||||||||| |||||||| ||||| || || || | |||||  | || |   || |    |    |   ||   | ||  | |     |  | ||  |  |  |||| |  |   ||  |    |  || ||||| |    
GCAGTTTTGAGGGCACTATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCGgtaatttgtgaattatttagctgaacttcttgttcttactagatgggtgcatattaaacatggagttgatgctttgtgcttattgacttgat-tgcaaata---

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 29
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaa--aactggcacatttgaattattttgccttctcctgaaagttca--tgatccacttaactcgtctcatgaatgtgcaattggta
|| || ||||| ||  |||||||||| ||||||||||| |||||||| ||||| || || || | |||||  | || |   || |    |    |   ||   | ||  | |     |  | ||  |  |  |||| |  |   ||  |    |   | ||||| |    
GCAGTTTTGAGGGCACTATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCGgtaatttgtgaattatttagctgaacttcttgttcttactagatgggtgcatattaaacatggagttgatgctttgtgcttattgacttggt-tgcaaata---

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: EFJ07288 (Selaginella moellendorffii), 5'ss of exon 18
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaaaactggcacatttgaattattttgccttctcctgaaagttcatgatccacttaactcgtctcatgaatgtgcaattggta
|| ||  |  |  | || ||||| |||||||| ||||  ||  ||||||||||||||||||| |||||||  | |  ||  |    |  |  | | |||     | |                                                           
GCTGTTCTTCGCTCCTTGTATGCCTACTTTGCGGACAAACCACTGAAAGAAATCCCACACATCGAGgtaatat-tttacgatcttgatttctcgcgtttagccgactacag-------------------------------------------------------

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: EFJ07831 (Selaginella moellendorffii), 5'ss of exon 18
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaaaactggcacatttgaattattttgccttctcctgaaagttcatgatccacttaactcgtctcatgaatgtgcaattggta
|| ||  |  |  | || ||||| |||||||| ||||  ||  ||||||||||||||||||| |||||||    |  ||  |    |  |  | | |||     | |                                                           
GCTGTTCTTCGCTCCTTGTATGCCTACTTTGCGGACAAACCACTGAAAGAAATCCCACACATCGAGgtaa-tgctttacgatcttgatttctcgcgtttagccgactacag-------------------------------------------------------

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|352764397|gb|FQ472754.1|FQ472754
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71882349|gb|DT031404.1|DT031404
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|352769630|gb|FQ468558.1|FQ468558
EST:     TATATGCTTACTTTGCTGACAGGCCTT-GAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71888454|gb|DT037509.1|DT037509
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|352768928|gb|FQ468119.1|FQ468119
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71889378|gb|DT038433.1|DT038433
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71887336|gb|DT036391.1|DT036391
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71887343|gb|DT036398.1|DT036398
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71890359|gb|DT039414.1|DT039414
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|34362375|gb|CF403960.1|CF403960
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71887083|gb|DT036138.1|DT036138
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|110360631|gb|EC923892.1|EC923892
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|110415443|gb|EC981352.1|EC981352
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|77581485|gb|DV219679.1|DV219679
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|352781433|gb|FQ468277.1|FQ468277
EST:     TATATGCTTACTTTGCTGACAGGCCTT-GAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71888451|gb|DT037506.1|DT037506
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71881182|gb|DT030237.1|DT030237
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|71885715|gb|DT034770.1|DT034770
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|27582400|gb|CB005095.1|CB005095
EST:     TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|352774206|gb|FQ474729.1|FQ474729
EST:     TATATGCTTACTTTGCTGACAGGCCTT-GAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
EST: gi|352768854|gb|FQ468045.1|FQ468045
EST:     TATATGCTTACTTTGCTGACAGGCCTT-GAAAGAAATCCCACACATTGAG                         GTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA
genomic: TATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatg ... cacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAGgtaaactatggacagttaaaaactggcacatttgaattattttgccttctcctgaaagttcatgatccacttaactcgtctcatgaatgtgcaattggta

- - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc