Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagttgtattaatttgatatatgctgcaactggtatgcttcatcccgtctcaactttttgtgtctcataaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC

Basic information

species Vitis vinifera
transcript Vv03s0038g00450.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g10130.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------gtaatagttgtattaatttgatatatgctgcaactggtatgc--ttcatcccgtct--caactttttgtgtctcataaatcc----cagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
                                                      | | ||     | |  |||          || || ||  ||   ||| |  ||||   ||| |||| |      ||||||     ||||||   ||||| |  || ||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| || || || ||||||||||||||| ||||||
gtatattgataattattctagtctggtgtttggcttttgacttgctgaatacaatcagagcatcctcaccttgtctggaaactcaccttgttggcaactcaccttgtctggaaacattttttacagtttaaatctattgcagAAAGTCAATATTACTCGGGATTACCTGGAGGACATAAATGAGATACCAAAATCACGCATGTTCTGGCCACGAGAAATATGGAGTAAATATGTTGACAAAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 3'ss of exon 6
-gtaatagttgtattaatttgatatatgctgca-actggtatgcttcatcccgtctcaactttttgtgtct---cataaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
  |  | ||||  ||  ||  ||   |  ||   |||   |   |  |     | | |        | |||   | || |   |||||||  ||||||||  | |||||| ||||||| ||||| ||||| ||||||||||| ||||| ||||| || || || |||||||||||||| || ||||
gttttttgttgattttgttgaatcagttatgtgcacttacagtttctaattgttgttagtaaccaatatctggacttacactgcagAAAATCAATATAATTAGGGATTATTTGGAGGACATAAACGAGATACCAAAGTCACGTATGTTCTGGCCTCGAGAAATATGGAGTAAATATGTCAATAAAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G029396_T02 (Zea mays), 3'ss of exon 2
-----------gtaatagttgtattaatttgat-atatgctgcaactggtatg--cttcatcccgtctcaactttttgtgtc---------------tcat-aaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
           |   |   || || ||    |   | |  |||  |  || ||   | || || || || |   ||||||||               |||| ||||| |||||||| ||||||||  | |||||| ||||||| ||||||||||| |||||||| |||||||| ||||| || ||||| |||||||||||||   | ||||
gtatgttaattggtctgaatgaatcaaccaaaccgtttcttgctccctgtgtgaaatgcaacctgtttcgagagtttgtgtcattaacaagtatttgtcatcaaatcgcagAAAACTAATATAATTAGGGATTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G108225_T01 (Zea mays), 3'ss of exon 6
-------------------------------gtaatagttgtattaatttgatatatgctgcaactggtatgcttcatcccgtctcaactttttgtgtctcat-aaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
                                  ||  ||   ||  | ||  | |||      ||| | ||     |  | |  | |     |   | |||| ||||  |||||||| || |||||  | || ||| ||||||| ||||||||||| |||||||| |||||||| ||||| || ||||| |||||||||||||   | ||||
gtatgtttattggtgtgaatgaatcaactgaaccattttttgcttcctgtgtgaaatggaatttctgttttgagattttgcattactaacaagtacttgtcatcaaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
-----------------gtaatagttgtattaatt-tgatatatgctgcaactggtatgcttcatcccgtctcaactttttgtgtctcat-aaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
                  || |||  || ||  || ||    |   ||   ||  |      |||    |   |  | |     |||  | | ||  ||||||||||| || || |||||||||||||| || || ||||||||||| |||||||||||||||||||| ||  |||||||||||||||||||||||||||
ttccctcctcctatatactattagaggtcttggttgtggctgaccttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 6
-------gtaatagttgtat-taatttgatatatgctgcaactggtatgcttcatcc-cgtctcaactttttgtgtctcataaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
        |  | || |||  ||||   | |||   |     ||  ||  || |    | | |||  |        ||   | ||  ||||||||||| || || |||||||||||||| || || ||||||||||| |||||||||||||||||||| ||  ||||||||||| |||||||||||||||
gtatcatatcgtggtagtaagtaataaaaaatacagtatggttgcaattgtttacttacatttcaggtcacc----ctttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTGAATATGTTAACAAAC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------gtaatagttgtattaatttgatatatgctgcaactg-gtatgcttcatcccgtctcaactttttgtgtctc----ataaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
                          |||  || |  |   |  | || |  ||||| |  | |   ||  |  | | | ||   ||| |  | |     | | |  ||||||||||| || ||| |||||||||| ||||| || |||||||| ||||| || |||||||||||||| || ||||||||| | ||||||| | |||| |
gtacaacaatgtattttgaggtgtacaatgtttcttcttcctcaa-atcttttgcaatttcggacaatttctatcat-tgaatgatttataacactggtcttatttgcagAAAACAAACATTATCAGAGATTATCTTGAGGACATTAATGAGATACCAAAATCCCGCATGTTTTGGCCTCGCGAGATTTGGGGCAAATATGCTGACAAGC

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 6
------gtaatagttgtattaatttgatatatgc------tgcaactggtatgcttcatcccgtctc---aactttttgtgtctcataaatc-----ccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
       | | | | |||| |  |||| || | |      |    ||   ||| ||  | |  |||    |   |||||| | | |||  |      | |||||||||| || |||  ||||||||| || || || |||||||  |||||||| |||||||||||||| |||||||||||| | ||||||||| ||||||
gtattcattacaatggtataatattgacatgtacaaggtttcttcctcaaatgttttttgcaatctttgaagtcttttgtatgttatatcttatttgctagAAAACAAACATTATCAAAGATTATCTTGAAGACATTAATGAGAGACCAAAGTCGCGCATGTTTTGGCCTCGTGAGATTTGGGGAAAATATGTTGACAAAC

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|33405611|gb|CF211238.1|CF211238
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110687328|gb|EE064642.1|EE064642
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATC
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATC
EST: gi|33402993|gb|CF208620.1|CF208620
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|351015968|gb|FQ431923.1|FQ431923
EST:     TGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: TGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110687067|gb|EE064151.1|EE064151
EST:     AAGATTTGGCTTCTGATGAACTCTCCCACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110699270|gb|EE076122.1|EE076122
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110710584|gb|EE087069.1|EE087069
EST:     GAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTAATTCTTCAA                         AAAACAA-TATA-TCCGAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAG
EST: gi|349815130|gb|FQ410353.1|FQ410353
EST:     TGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: TGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110700987|gb|EE078120.1|EE078120
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAAAATA-TCCGAGATTATCTGGAAGATATAAA
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAA
EST: gi|110693784|gb|EE070316.1|EE070316
EST:     AAGATTTGGCTTCTGATGAACTCTCCCACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110688718|gb|EE067590.1|EE067590
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|34546786|gb|CF515018.1|CF515018
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|22007996|gb|BQ793030.1|BQ793030
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|33405294|gb|CF210921.1|CF210921
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110729518|gb|EE105539.1|EE105539
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
EST: gi|110369584|gb|EC933748.1|EC933748
EST:     AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAG                         AAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG
genomic: AAGATTTGGCTTCTGATGAACTCTCCAACTCAATGGGTTTATTTCTTCAGgtaatagttg ... taaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgcaactggtatgcttcatcccgtctcaactttttgtgtctcataaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC
                             aacttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatagttgtattaatttgatatatgctgcaactggtatgcttcatcccgtctcaactttttgtgtctcataaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG