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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggcccaacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc...

Basic information

species Vitis vinifera
transcript Vv08s0105g00590.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 5'ss of exon 4
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggcccaacatttatgctg---aacatt--tttgctcttacttggaatttgttaaatctttc
 | | |||||||||||| ||||||||||| ||||| || || ||||| ||| | || ||||||||| |||||||||| ||||| |||||||   ||| |||   ||  | | || || || || |  |    |     |   || | ||    || | |  ||||  |     | ||||| || || |  || 
GACATATGGAAGATTCGCCTTCAACTTACTAAGCCAGTGACATGGCCTCCGCTTGTATGGGGAGTGCTTTGTGGAGCAGCTGCCTCTGgta---tgcctatg-gtacctttcgttgattttatctgtttggagagtttattcttctacttcctaataatcatttgagcacctgtagaattggtaaactactt-

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggccc---aacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc-
 | | ||||||||| |||||||||||||| ||||| || || ||||| ||| | |||||||||||  | |||||||| ||||| |||||||   |||||   |   |||| ||    ||   | ||| |||||  ||   ||   || ||     |   ||       ||      | |  |  || |||| 
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgta---tgctttgctgcctataatggtttatgtctgtta-ctctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G19340.1 (Glycine max), 5'ss of exon 1
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggcccaacatttatgctgaacatttttgctcttacttgg-aatttgttaaatctttc--------
|||||||||||||||||||||||||| ||||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| || ||||||    |      |||  | |       |||| |||   || | |   |||||   || || || |||| || | | |   ||| || ||| | |||         
AATAAATGGAAGATTCGTCTTCAACTCACAAAGCCTGTCACTTGGCCTCCGTTAGTTTGGGGAGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaattc-----tatcaactagca---taatgttaaaacttgacatgcattttcactaaa-atgtttggtcctgcatattaatgtgataattgtttacacatgtt

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G43310.1 (Glycine max), 5'ss of exon 4
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatat----tatctctggcccaacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc
||||| ||||||||||||||||||||||||||||| || |||||||| || || |||||||| || |||||||||||||||||||||||||||    |  |||  || ||   |   ||||| ||     ||   ||| |  | |   |   ||  | |   || || |  |   ||||  ||| |  | | 
AATAAGTGGAAGATTCGTCTTCAACTTACAAAGCCAGTCACTTGGCCTCCATTAGTTTGGGGTGTAGTTTGTGGAGCTGCTGCTTCTGgtactaaattc-tatcaat-tagcataacattaaaatgtgacatgcatggtcacaaaaaaa-attggtcctgcatgttcctg-tgataattgtttacacatgtt

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 4
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggcccaacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc--------
|||||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||| || |||||||| |||||||| || ||||||    |      |||  | |       |||| |||   || | |   |||||   |  ||   ||| |  |||  |   ||| || ||| | |||         
AATAAATGGAAGATTCGTCTTCAACTCACAAAGCCTGTCACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaattc-----tatcaactagca---taatgttaaaacttgacatgcattttcacaaaaatgtttggtccttcatattaatgtgataattgtttacacatgtt

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 5'ss of exon 4
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggcccaacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc--
||||||||||||||||||||||| |||||||| || || |||||||| ||  ||||||||||||| || ||||| ||||||||||| |||| ||     |||   |  | || ||||              |    ||| | |  | | |||  ||||| |  || | |   | |||||   |||  |  
AATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAGgtaatc-----atacgaacctcttttgga--------------tcatgcaatact-gtacagaaagttttttcattttccttccaattgtttcttctggcag

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|34547700|gb|CF515932.1|CF515932
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|30252103|gb|CB968742.1|CB968742
EST:     TGCTGCTTCTG                         GG-ACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351018952|gb|FQ426451.1|FQ426451
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATTTATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|161709684|gb|FC060175.1|FC060175
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTG
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTG
EST: gi|352785482|gb|FQ477696.1|FQ477696
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCCGCCTCCG                         GGAACTTCCAAAGGAATTTGGAGGATGTTGCC
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCC
EST: gi|349830671|gb|FQ416969.1|FQ416969
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|161716004|gb|FC065529.1|FC065529
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351033623|gb|FQ447782.1|FQ447782
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351041270|gb|FQ447397.1|FQ447397
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351034199|gb|FQ463133.1|FQ463133
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351025946|gb|FQ427958.1|FQ427958
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351031189|gb|FQ445016.1|FQ445016
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|352791138|gb|FQ477465.1|FQ477465
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351028530|gb|FQ444811.1|FQ444811
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|349833147|gb|FQ416525.1|FQ416525
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCACTTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351014975|gb|FQ444264.1|FQ444264
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351017844|gb|FQ436197.1|FQ436197
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|110712697|gb|EE087971.1|EE087971
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|110698374|gb|EE075807.1|EE075807
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|351018561|gb|FQ424668.1|FQ424668
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
EST: gi|349829107|gb|FQ419639.1|FQ419639
EST:     TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG                         GGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA
genomic: TACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgct ... cacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggcccaacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT