T-DNA Express: Arabidopsis iSect Tool ( Aug. 2, 2016 )


1.Preferences :
Click to edit your preferences.
2.
Search :
 Type:               Query:   
3.
Locate :
 Chromosome:    Position: 
4.
Fetch  :
 Chromosome:    Coors:   
UTR 5':   UTR 3':   Promoter:  
5.
mText :
Type:           
Please paste your list:


6. iSectR :
Chromosome:    Strand:
Range :  
Intron:      Ext 5':    Ext 3':  
7.
iSectL :
Please paste your list:
Intron:   Ext 5':   Ext 3':  
8. PrimerL :
Primer size - Opt: Min: Max:
Primer TM - Opt: Min: Max:
GC Content - Min: Max: Clamp:
Max N: Ext5: Ext3:
Primer Zone:  BPos:
Data Type:  Format:  

Please paste your list:


9. PrimerS :
Primer size - Opt: Min: Max:
Primer TM - Opt: Min: Max:
GC Content - Min: Max: Clamp:
Primer Zone - Left: Right: Format:     

Please paste your sequences:


  • 1. Preferences : Edit your preference to set your own values of the image width, the zoom factor, UTR regions and promoter, to hide or show a set of data, as well as to change display shapes, sizes, colors and track spans instead of default settings. It has less priority than the iView Tool.

  • 2. Search : To open a browser window by querying a gene, a BAC, or data (cDNA, T-DNA) and function. For example: AT1G01010.1 or SALK_001127.50.70.x.

  • 3. Locate : To open browser window by positiohing its location (chromosome and position).

  • 4. Fetch : To retrieve all displayed data from a chromosome region. For example: 1234-2345 or W/1234-2345.

  • 5. mText : It is now evolved to accept multiple search for both gene list or cDNA/T-DNA/other list to retrieve related or hited data or genes. For example: 
    	please choose type: Gene for gene list or Data for cDNA/T-DNA list.

	AT1G01010.1
	ATMG00640.1

	or

	SALK_001127.50.70.x
	SALK_071005.54.25.x
  • 6. iSectR : iSect (R) tool to retrieve sequence from a specific chromosome region. For example : 1234-2345 or 1234-2345,3456-4567.

  • 7. iSectL : iSect (L) tool to retrieve sequences from genome by list of data names or list of genome mapping data. For example: 
    	AT1G01010.1
	SALK_001127.50.70.x
	SALK_071005.54.25.x

	or

	query1 chr1 0.0 W/1234-2345
	search2 chr2 0.0 C/1234-2345,3456-4567
  • 8. PrimerL : iSect primer (L) tool to design primers according to a list of data names existed or a list of genome mapping data. For example: 
    	AT1G01010.1
	SALK_001127.50.70.x
	SALK_071005.54.25.x

	or

	query1 chr1 0.0 W/1234-2345
	search2 chr2 0.0 C/1234-2345,3456-4567
  • 9. PrimerS : iSect primer (S) tool to design primers from user input sequences. For example: 
    	>YourInput.fa
	CTCGCTGGCCTGTTCAGGTGAATCTTAGTATCGTTTTGTGTCCATGTTGCCTCTACTTCG
	CCTGCTTCTGGTGACTTGAATTCTCTCTTTGTTTTGGGCAGCTTCGGGAACCTTCCACAT
	CCGAAGATGCTGAATTCGCTTCTATTTTGCGGACTCTCAAGGACAGTTTTGATAACGCAT
	TCACTGCTATGATTTCCTTCCAGACGAAGAATTCCGAGCGCATATTCAGCACAGGTATAA

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