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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag

Basic information

species Vitis vinifera
transcript Vv19s0015g01730.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgtt-ggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||||||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| || |||||||| || || ||  | |||||| ||    ||||   | |  |  |||  ||||      |   || |   ||||  | | ||  | |    |                                                    
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattat--ttgttggagttagtcaaat-tactaagctcttgattccttgcag---------------------------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacac-actacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||||||||||||||||||||| ||||| ||||| || |||||||| |||||||||||||||||||| || || ||||| || || ||  | |||||| |     |   |||   | |||||  ||   |    |  |   |||  |||   | | ||  | |    |                                                    
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAGgtttggt---ttaatctacttttgtattgtttgttggagttaagtcacattactgagctcttgattccttgcag---------------------------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatct-ctctctctctgtatccttgtctccca---tgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||| || || ||||||||||| || |||||||| || |||||||| || ||||||||||||||||| ||| ||||||| || || || || |||||  ||   |||  || |  |  ||| |    ||    ||   | |  |||   | |       ||||                                                            
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag-----------------------------------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||| || ||||||||||||||  | || ||||| || |||||||| || ||||||||||||||||| ||| ||||||| || || || || |||||  | |  |||   || |  |  | |  | |  |       |     |   |  | |  |   ||||                                                        
TGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAGgtctggcttatcaa-cttttgccatgtgttagggtgagtcaaattactaagatctaaatttctttgcag-------------------------------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA14G01480.1 (Glycine max), 5'ss of exon 9
------TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
      ||| ||||||||||| |||||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| ||||| || || ||||| |||||| | ||          | |  || | ||||  |    ||    ||  || | ||      |   |   |   | | | |  |     ||       |   || |  ||  || | ||  |||
TTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtca----------tttgcgtgtgcttgggtatactgttttgattcatttcatgatcactaactt-gtcctgttttttttggtgattca----ctaacttgtcctttgattattgagcag

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G47270.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||| ||||||||||| |||||| | |||||||| |||||||||||||| |||||||| |||||||| ||||| ||||| || || ||||| |||||| | ||      ||| | | |||      || | ||     | ||  || | ||   ||     |||   | ||| | |  |    |  |      |   || |  ||  || | ||  |||
TGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtca------tctgtgtgtgtgcttgggtatacctgtgtcggattcatttcatg-at-----cactagtgtcttttttttttggtgat--tcactaacttgtcctttgattattgagcag

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA18G08180.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||| ||||||||||||||||||||| ||||||| || ||||||||||| |||||||| ||| | || || || ||||| || || |||||||||||| |           |   |||| |||  ||  |     | ||| |         ||  ||     || || ||||        |   ||||| |  |  |                      
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGGttag-----------ttcatctgcatctatggtttg---gtacaaatctctgtttcatttggtgatactgacatctt-------atgctttgattaatgatcagc------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G45270.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||| ||||||||||||||||||||| ||||||| || |||||||| || |||||||| ||| | || || || ||||| || || |||||||||||| |           |   |||| |||  ||  |     | ||| |         ||| ||     || |||||||        |   |||||    |  |                      
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGgttag-----------ttcatctgcatctatggtttg---gtacaaatctctgtttcacttggtgatactgatatctt-------atgctttgatcaatgatcag-------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
 ||||||||||||||||| ||| |  ||||||| |||||||| |||||||||||||||||||| || ||||| ||||| || || ||||| |||||| |       ||| |||||    |||  | ||||| |   |   ||  || ||| |   |||  |||       ||||||| |  |                                    
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtg----ttctttctctgctcatcact-tctcctaactatttactaacaacaaatg-gcactcaccagc--ttatctacgagaag-----------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
 ||||||||||||||||| ||| |  ||||||| |||||||| |||||||||||||||||||| || ||||| ||||| || || ||||| |||||| |       ||| |||||    |||  | ||||| |   |   ||  || ||| |   |||  |||                                                       
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtg----ttctttctctgctcatcact-tctcctaactatttactaacaacaaatg-gcactcaccag----------------------------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
||||||||| ||||||||||| || ||||||||||||||||||||||| || |||||||| || || || || ||||| || || ||||| |||||   ||   || |||    |   | |||  || | |  ||      |||  |  |    || ||        |                                                  
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgt-aaacgagtcactcctatttcat-tccaggtgttc--tgtttcatcactgttgatgtctgtatcactgtgcag-------------------------------------------------

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S488_8V6.1 (Physcomitrella patens), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag---------------------------------------------------
||| ||||| ||||||||||||||||| || ||||||||||| || ||  |||| || ||| | || |||||||| || ||| | ||  |||||||   ||   |      | ||  || |   |||| | | |          |      |  ||  | ||  || |||| | | |  |  | ||||  |||  || | |  |  |  |    | ||                                                   
TGGAGAGAGCATGGAGAATGCTTTGCGTGCGTGTTGCAAAGGCATTAAGGTTGGAAAAATTTTGATTCATAGGGAGGGAGATGATGGAAAGCAGgtactacttgtgagatgcccttggt-taaatgtcacgcttatttctctttatcttctagttgttttcaatga-atctctgtcccgaggtgttga--gttaattcaaggctgcacaatgtcaaagaggttgatagtgtttgtgctcatctataaaatgtggttgattataatgcag

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgt--tggacagatctctctctctctgtatc---cttgtctccc---atgcacagacacactacacaca-tgcatgcacagatatcta-tctactaacattttgactgtttttttatgtttcaatgactggacag--------------------------------------
||| ||||||||||||||||||||||| || |||||||| || ||||| ||||| |||||||| || ||  |||| || ||| ||||  |||||||  | |   ||| |   |     ||||||   ||||  |  |   ||      | |   |  | ||  || || |  | || |  | |  | | |    |  || |  |    |   || || |  ||||                                         
TGGAGAGAGTATGGAGAATGCTTTGCGGGCGTGTTGCAAGGGCATCAAGATTGGAAAGATTCTAATACACCGGGAGGGAGATGACGGGAAGCAGgtacttgttggatgtgattggtcttgtatcacgcttgcttttcttcatcttttcatattttcaatacgctgaatccgaatatgttaagttcattcaaggctgcacagaatcgcaaatgttgaaagtttggagctacttcatctgttaaaagtggctgatggtgatgatgcag

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|349818455|gb|FQ401069.1|FQ401069
EST:     TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG                         CTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
genomic: TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacaga ... gactggacagCTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
EST: gi|349825804|gb|FQ423099.1|FQ423099
EST:     TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG                         CTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
genomic: TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacaga ... gactggacagCTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
EST: gi|349832612|gb|FQ421970.1|FQ421970
EST:     TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG                         CTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
genomic: TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacaga ... gactggacagCTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
EST: gi|349808312|gb|FQ405456.1|FQ405456
EST:     TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG                         CTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
genomic: TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacaga ... gactggacagCTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
EST: gi|349824583|gb|FQ413250.1|FQ413250
EST:     TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG                         CTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
genomic: TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacaga ... gactggacagCTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
EST: gi|349809963|gb|FQ398588.1|FQ398588
EST:     TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG                         CTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC
genomic: TCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacaga ... gactggacagCTAATCTATGAAAAACTTCCAAAAGATATCTCAGACAGGCATGTGTTACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA