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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttcactctgacaactctgtaggttttgcatttgtttatttggaagattatggttgtaggctgaagtaattgttctcttggcatttctctct...

Basic information

species Vitis vinifera
transcript Vv17s0000g05800.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 5'ss of exon 10
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttcactctgacaactctgtaggttttgcatttgtttatttgg--aagattatggttgtaggctgaagtaattgttctcttggcatttctctct---
|| || ||  |||||||||| || || || ||||| ||||| |||||||| || ||||||||||| ||||| ||  ||||||||||  |||| |  |  |  |   |   |  | |||   || |    |||  | ||||     ||| |||  | | | |  |  ||| |  | |       ||  | | |   
GTTGATTACATTGCATGGGTTTGCGACCAGGATGCTTATGCTTGCAGTGGTCAGAAGTGCTCTGCTCAGTCTATTCTATTCATGCACAAGgtaa--tagtgaagattagta-ttatgttccttctttgcttgagtctttgactgtgatcatgactcttgac--atataacttatgttacatgcttcttttttatc

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA05G01290.1 (Glycine max), 5'ss of exon 10
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgc----ttcactctgacaactctgtaggtt-ttgcatttgttta----tttggaagattatggttgtaggctgaagtaattgtt-ctcttggcatttctctct-------------------------------------------------------
|  || ||  | || |||||||||||||| |||||||||||||||||||| || || ||||| || |||||| |  |||| |||||||||||  | | |     | | | ||| |||| |||   |  ||  || |    |     |  |  ||  |||    || |   |     || ||  | ||   ||   | |                                                         
GAAGATTACATAGCCTGGGTCTGTGATCAGGATGCATATGCATGCAGTGGTCAGAAATGCTCGGCACAGTCATTGTTATTTATGCATGAGgtctgttacattggttattatgagaactttgttcatgattaaatgtccccaagaactacggggaagatgtacataagtacattgggtttttatttttaatatgcatgttacgagtttatgtatcgtgtctttactaacttcatggtttggatttcccttgttcag

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA17G10610.1 (Glycine max), 5'ss of exon 11
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgc-ttcactctgacaactctgtaggttttg--catttgtttatttggaagattatggttgtaggctgaagtaat-tgttctcttggcatttctctct-------------------------------------------
|  || || || ||||||||||||||||| |||||||| ||||||||||| || || ||||| || || ||| |  |||| |||||||||||| | | | ||   | | |  | |   | | |  ||   |  |||      | |  |   ||||| |    |   ||| | ||  || |  |  ||| | | |                                           
GAAGATTACGTAGCATGGGTCTGTGATCAGGATGCATACGCATGCAGTGGTCAGAAATGCTCAGCACAATCATTGTTATTTATGCATGAGgtttgttacattggttattatgagtactttgttcatgactaaatgtccccaagaactacattggtttttttattttgtattatgcactttatgagtttatgtattgtgtcattactaacttcatggtttgaattttcccttgttcag

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA05G01300.1 (Glycine max), 5'ss of exon 11
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttc----actctgacaactctgtaggttttgcatttgtttatttggaagattatggttgtaggc-tgaagtaattgttctcttggcatttctctct--------------------------------------------------
|  || ||  | || |||||||||||||| |||||||||||||||||||| || || ||||| || || ||| |  |||| |||||||||||  |   | |     | | | | ||||   |    |||  || |  | |      ||  |   | || ||   || | |  || ||   || | |     | ||                                                  
GAAGATTACATAGCGTGGGTCTGTGATCAGGATGCATATGCATGCAGTGGTCAGAAATGCTCAGCACAATCATTGTTATTTATGCATGAGgtctgtcacattggttattttcagaacttgttcatgtttaaatgtcctcaagaactagggtgaagatgaagatgtgcaattgttatttattttgtaagatgcactttacgcattgcatctttactaacttcaggatttgaatttcccttgtttag

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G62530.1 (Arabidopsis thaliana), 5'ss of exon 11
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttcactctgacaactctgtaggttttgcatttgtttatttggaagattatggttgtaggctgaagtaattgttctcttggcattt-ctctct------
|| || ||||||||||||   ||||||||||||||||| || ||||||||||| ||||| ||||| ||||| ||  | ||  | ||||||||| | |   | |  || |    | ||  |    | | ||||  | ||| |   | |    || |   |||   |  ||||| ||   | |||| ||||||      
GTTGATTATGTTGCATGGCAATGTGATCAAGATGCATACGCGTGCAGTGGACAGAAGTGTTCTGCACAGTCTATGCTTTTTGTTCATGAGgttggtt---tgatcctaattgttatggtgaaactacctttgaatcttttgtttacttccattttcttctgtctttgttgttttcaatgtattttctctctgagcag

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S41_177V6.1 (Physcomitrella patens), 5'ss of exon 12
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgtt--agctgcttcactct----------------gacaactctgtaggttttgcatttgttta--tttggaag-attatggttgtaggctgaagtaattgttctcttg-gcatttctctct---------------------------------------------------------------
| |||||||||||| ||||| ||||| || || || || || |||||||||||||| ||||| || || |||||| |||| ||||||||||||  |  | | |  || |                | ||| ||| |    | | |||   | ||  | ||  || ||||| | ||||       | | | |   |     ||||||   |                                                                 
GAGGACTATGTTGCGTGGGTGTGTGACCAGGACGCTTACGCTTGCAGTGGACAAAAATGCTCAGCACAATCAATACTATTTATGCATGAGgttccatatacatttcttttagagcatgttttcgaggcaattcttttaaatgtacatggatctagctctgagagtattattgctgtacatcattgaagtcgacttaaaaagcattttgttagttgaccaacttggtcttttacaataagtccatatctgtgatgtccatattttcttcgttgcag

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ29772 (Selaginella moellendorffii), 5'ss of exon 10
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttcactctgacaactctgtaggttttgcatttgtttatttggaagattatggttgtaggctgaagtaattgttctcttggcatttctctct
 | ||||| ||||||||||| || || || ||||||||||| |||||||| || ||||| || || ||||| ||  | |||||||| |||||    | ||    ||| | | ||  | |||   || |      || ||| |                                                
ATTGACTACGTTGCATGGGTTTGCGACCAGGATGCATATGCGTGCAGTGGTCAGAAGTGTTCGGCACAGTCCATTCTTTTCATGCACGAGgtcga-tactgttttcttaaagcta-gcaggagctgaaaagccgtagttgcag-----------------------------------------------

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ08918 (Selaginella moellendorffii), 5'ss of exon 10
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttcactctgacaactctgtaggttttgcatttgtttatttggaagattatggttgtaggctgaagtaattgttctcttggcatttctctct
 | ||||| ||||||||||| || || || ||||||||||| |||||||| || ||||| || || ||||| ||  | |||||||| |||||    | ||    |||          ||   || |||   | |||     ||     | |||| ||                                 
ATTGACTACGTTGCATGGGTTTGCGACCAGGATGCATATGCGTGCAGTGGTCAGAAGTGTTCGGCACAGTCCATTCTTTTCATGCACGAGgtcga-tactgttttct----------taaagttagcaggagctta-----aaagccgtagttgcag---------------------------------

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|33402546|gb|CF208173.1|CF208173
EST:     CATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAG                         AACTGGTTTAAAAGTTCACTTATTTCCAGAATGAAAGATCTTGCTGCAAGA
genomic: CATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgct ... tcttatgcagAACTGGTTTAAAAGTTCACTTATTTCCAGAATGAAAGATCTTGCTGCAAGA
EST: gi|110380514|gb|EC945785.1|EC945785
EST:     CATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAG                         AACTGGTTTAAAAGTTCACTTATTTCCAGAATGAAAGATCTTGCTGCAAGA
genomic: CATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgct ... tcttatgcagAACTGGTTTAAAAGTTCACTTATTTCCAGAATGAAAGATCTTGCTGCAAGA
EST: gi|110731235|gb|EE109223.1|EE109223
EST:     CATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAG                         AACTGGTTTAAAAGTTCACTTATTTCCAGAATGAAAGATCTTGCTGCAAGA
genomic: CATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgct ... tcttatgcagAACTGGTTTAAAAGTTCACTTATTTCCAGAATGAAAGATCTTGCTGCAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGACTATGTTGCATGGGTCTGTGATCAAGATGCATATGCATGCAGTGGACAAAAGTGCTCTGCGCAGTCAATAGTATTCATGCATGAGgttagctgcttcactctgacaactctgtaggttttgcatttgtttatttggaagattatggttgtaggctgaagtaattgttctcttggcatttctctct

- - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctctc