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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag

Basic information

species Vitis vinifera
transcript Vv02s0025g03370.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 9
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgtttt---ttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
 || || ||||| ||||||||||| || ||  |||||||  | || ||||| ||||| |||||||||||  |||||||||| |||||||| |||||||||||  | | | | | | |  | ||    | | ||  |  | ||      |  ||   | |||| |  | |  |  | |     |  ||     |||  | ||   |                                                           
AAATTCTAATGGATGTAATCTTGCTGTTGACATATGGAGCTTAGGATGCACGGTTTTAGAGATGGCTACCTCAAAACCACCATGGAGCCAATATGAAGGGgttagtacttatactaggctcttaagctgtattttatgtttttgtgcaacacacattttcttttcatgagaaggtactccctttggt-----cataaatatttga-----------------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 5'ss of exon 9
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
 ||||||||||| || || || || || ||  |||||||| | || ||||| ||  |||||||||||||| | ||||| || ||||||||||||||||||||  | ||| | | || ||      | |||     |  |  | |  |   |      || | || | | |   |||   | | || ||  || || ||| |                                                            
AAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGTATGAAGGGgttagtatt-atacttctgaggcacagtttatttgttctataatatagataacctaattatggtgattttcgccatgagtgaatggga-tatggaaatgttc-----------------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G093316_T01 (Zea mays), 5'ss of exon 9
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
 ||  | | ||| ||||| |||||||| ||| |||||||| | || ||||||||  | |||||||||||  |||||||||| |||||||| |||||||||||  |  ||  |  ||     | | ||||      | || |   || | ||  |   ||  |      | |    ||| | ||   |    ||    | |  |  |                                                       
AAATGCTAGTGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAATATGAAGGGgtcagtgttagactttacagctataattt-----gtgtttc-tgtagtgaaatttcgttgctagggtaacacat-tatattagaatgcatcttttttttcctgctaa------------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AC209208.3_FGT001 (Zea mays), 5'ss of exon 8
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctca-gtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
 ||  | |  || ||||| |||||||| ||| |||||||| | || ||||||||  | |||||||||||  |||||||||| |||||||| |||||||||||  |  ||  |  ||     | | ||||      | || |   || |   |   | |  ||| |   |   ||| |  | | |  |||    |||    |      | |                                                    
AAATGCTAGCGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAATATGAAGGGgttagtgttagactttaaagctatgattt-----gtgtttc-tgtagt--gtaaatttgattgcag--agggtcacacattatgcaagatgtatgatgcacctttttttc----------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G175504_T01 (Zea mays), 5'ss of exon 8
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatca-atgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
 || || ||||| || || ||||  || ||  |||||||| | || ||||| ||  |||| ||||||||  |||| ||||| ||||||||||||||||||||  | |||  | ||     | |  |  |   |  | ||  |     ||| ||||||  |  |  | ||   || |            |   ||||| |  |                                                            
AAATTCTAATGGATGCAACCTTGTGGTTGACATATGGAGTTTAGGTTGCACTGTCCTGGAAATGGCTACCTCAAAGCCACCATGGAGCCAGTATGAAGGGgtcagtattagacatcacaatat--aactgatatttcttctagagtgtcagatgtctggtgctcaagctgagttaaccatctgcatttattgttgac-tattg-----------------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA08G01880.1 (Glycine max), 5'ss of exon 8
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttcca-aatattgcactta-atc---aatgtctcttcttgtaactatattcatatctcagt-gagagcattga---catgctagacatactggagtg--tgcttgacccattttttctcttacattctaccttcttctccaaag
 || |||||||| ||||||||||| || ||| |||||||||| || ||||| |||||||||||||| ||||||||||| ||||||||||| |||||||||||  |  | ||||            || ||  | | | ||| |  || ||    ||| | | ||||   |   ||||    |||| ||| | || | | ||   |||||| | |       | ||  ||| | ||   ||| | || ||  |  |||| |  |||    |||
AAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAATATGAAGGGgtgagtttgcaaacagactaaaagcatcttgaacattgttgtatgtacatttgaaatctattttctgacacaaatatatgaatcttagttgggaacttagagcacatgcttgtctagaaacattgattgcataacttgtttctgctgttttacactacatgtttc----aag

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA11G02520.1 (Glycine max), 5'ss of exon 11
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
||| |||||||| ||||||||||| || ||| ||||||| ||||| | ||| ||||| ||||||||||| |||||||| ||||||||||| || ||||||||  |       |||| ||      |  |   ||| | || |           |  | | | | || |||||  || |||  ||  |||||    |||| | |  ||||   | ||| | |  | ||| |||  |  | |   |   || | | |      
GAATTCAAATGGTTGTAATCTTGCTGTTGATATATGGAGCCTTGGCTCCACCGTTTTCGAGATGGCTACTACAAAACCTCCTTGGAGCCAATACGAAGGGgtgag-----ggaattttgacaacaaactagaaaagactgaa-----------taccgtttagaaaatatatgaatctctttgttggagca----catgtttg-tatac---aatgttcattgctcatctttctttcttctgccgtactacatgttag---

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA01G42960.1 (Glycine max), 5'ss of exon 8
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcac-ttaatcaatgtctcttcttgta---actatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctctta-cattctaccttcttctccaaag
 || |||||||| ||||||||||| || ||| ||||||| ||||| |  || ||||| ||||||||||| |||||||| ||||||||||| || ||||||||  |       |||  ||      |  |   ||| | || |    | |  || | | ||||  ||   | |||||  || |||  ||  |||||    |||| | |  ||||   | ||  | |  | ||| |||  |  |  | | |||| |  |         
AAATTCAAATGGTTGTAATCTTGCTGTTGATATATGGAGCCTTGGCTCTACCGTTTTTGAGATGGCTACTACAAAACCTCCTTGGAGCCAATACGAAGGGgttag-----ggaatattgacaacaaactagaaaagactgaataccatttcatatattttctgataaaaaatatatgaatctctttgttggagca----catgtttg-tatac---aatgctcattgctcatctttctttctgtcgtactacatgttag-------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 5'ss of exon 8
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatca-atgtctcttct-tgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
||| ||||||||| |||| ||||| |||||  ||||||||||||| || || ||||| || ||||||||||| ||||| || ||||||||||||||||||||  | |     |||  | |   | | |   |||| ||   | | ||| |   | ||||||  |     | |||||   |       ||                                                                          
GAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGTATGAAGGGgttagta-----aatcatataagt-actcaacaaacatgagattgaatgatgcgactcttccatccttatgtattcgagttctttacag--------------------------------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ36728 (Selaginella moellendorffii), 5'ss of exon 6
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
  |  || |||| |   ||||  | || ||  | ||||| ||||| ||||| ||| |||||||||| ||| |||| || || |||||||| |||||||||||  |       |  | |||  ||   ||| | | |  | |   |||| | |  ||  |||   |                                                                                                
ACAAACACATGGATACGATCTCTCTGTGGACGTTTGGAGCCTTGGCTGCACGGTTCTGGAGATGGCGACAGCAAAGCCTCCATGGAGCCAATATGAAGGGgtcagtt-----acctttgtccttcgcttttccatttcttctgctaat-agttacttctctctcag-----------------------------------------------------------------------------------------------

upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ27940 (Selaginella moellendorffii), 5'ss of exon 6
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgt-aggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag
  |  || |||| |   ||||  | |||||  | ||||| ||||| ||||| ||| |||||||||| ||| |||| || || |||||||| ||||||||||| ||  |  |       |   ||||   || |   |  |||   || | | | |||||    |                                                                                                  
ACAAACACATGGATACGATCTCTCTGTCGACGTTTGGAGCCTTGGCTGCACGGTTCTGGAGATGGCGACAGCAAAGCCTCCATGGAGCCAATATGAAGGGgtcagttaccctcgtccttcgcttttccatttcttctgctgctaatagttact-tctctctcag--------------------------------------------------------------------------------------------------

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|349822931|gb|FQ399910.1|FQ399910
EST:     CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGG                         GTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
genomic: CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattc ... ttctccaaagGTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
EST: gi|351026069|gb|FQ428081.1|FQ428081
EST:     CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGG                         GTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
genomic: CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattc ... ttctccaaagGTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
EST: gi|349829212|gb|FQ419744.1|FQ419744
EST:     CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGG                         GTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
genomic: CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattc ... ttctccaaagGTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
EST: gi|349817348|gb|FQ405352.1|FQ405352
EST:     CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGG                         GTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
genomic: CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattc ... ttctccaaagGTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
EST: gi|351054267|gb|FQ450349.1|FQ450349
EST:     CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGG                         GTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
genomic: CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattc ... ttctccaaagGTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
EST: gi|351028430|gb|FQ427326.1|FQ427326
EST:     CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGG                         GTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT
genomic: CAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattc ... ttctccaaagGTTGCTGCTATGTTTAAGATTGGTAACAGTAAAGAACTTCCCACAATACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGTATGAAGGGgtaggcattcaaaattgtgttttttattttccaaatattgcacttaatcaatgtctcttcttgtaactatattcatatctcagtgagagcattgacatgctagacatactggagtgtgcttgacccattttttctcttacattctaccttcttctccaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG