Gene Tools Oligo Design Form

Customer Information

Email address *

Your name *

Your institution

Enter temperature (°C) at which oligo(s) will be exposed to RNA (e.g. temperature of body, aquarium or incubator) *

Common temperatures:

Zebrafish 26°C
Xenopus laevis 16°C to 22°C
Xenopus tropicalis 25°C to 30°C
Mouse 37°C
Human cell culture 37°C

Choose which type of Morpholino oligo you would like us to design *

Translation blocking (mRNA target)

Splice Modifying (pre-mRNA target)

miRNA Inhibiting

RNA Target Protector (not splice modifying or translation blocking)

Other

Choose which type of Morpholino: Other *

Validate your oligo

5-mispair Control (not recommended)

Unusual oligo not listed above

Translation Blocking Oligo, mRNA Target

Select the kind of target mRNA sequence you can provide *

mRNA sequence, 5' UTR through 25 bases of coding sequence with start codon marked (ATG)

Ensembl mRNA transcript ID (e.g. ENSDART123123123)

GenBank mRNA transcript (e.g. NM_123123)

Translation Blocking Oligo -> mRNA sequence 5' UTR

Choose a name for your oligo *

Enter the 5'UTR sequence plus 25 bases of the coding region with the start codon marked with parentheses (atg) *

If you have additional information for this design, enter it here

Translation Blocking Oligo -> Ensembl mRNA transcript ID

Choose a name for your oligo *

Enter the Ensembl transcript ID (Example: ENSGALT00011122233.3) *

If you have additional information for this design, enter it here

Translation Blocking Oligo -> GenBank mRNA transcript

Choose a name for your oligo *

Enter the GenBank mRNA transcript ID *

If you have additional information for this design, enter it here

Splice Modifying Oligo, pre-mRNA Target

Choose whether you will provide splice junction sequence or a database accession number *

Up to 6 intron-exon or exon-intron boundaries (50 bases each boundary)

Ensembl mRNA transcript ID and target exon number(s) (Up to three exons can be targets per request)

Splice Modifying Oligo -> Up to 6 intron-exon or exon-intron boundaries

For each target splice junction enter 50 bases with 25 bases exon sequence in UPPER CASE and 25 bases intron sequence in lower case. Note that the sequence fields only accept up to 50 characters.

Oligo Name *

Sequence 1 *

Oligo Name 2

Sequence 2

Oligo Name 3

Sequence 3

Oligo Name 4

Sequence 4

Oligo Name 5

Sequence 5

Oligo Name 6

Sequence 6

Additional Info

Splice Modifying Oligo -> Ensembl mRNA transcript ID and target exon number

Choose a name for your oligo *

Enter the Ensembl transcript ID (Example: ENSGALT00011122233.3) *

Target Exon

You may specify up to three exons or you may leave this blank and we will choose a target exon.

Target exon number(1)

Target exon number(2)

Target exon number(3)

If you have additional Information for this design, enter it here

MicroRNA Inhibiting, miRNA Target

Choose a name for your oligo *

Enter miRBase ID or miRBase name (e.g. dre-mir-123 or mi1234567) *

If you have additional information for this design, enter it here

RNA Target Protecting Oligo

This can be an oligo targeting a miRNA response element, a protein binding site as for a splice regulatory protein (e.g. SR protein), or any other interaction with the base pairing surface of an RNA that occurs at a known, limited region.

Choose a name for your oligo *

Provide sequence in upper case text centered on the area you wish to block, writing the bases in that area in lower case. Ideally send 60 bases, though we can try with as few as 25. *

Example: "AAGACAGGCGAGgcagcccaCTTAGTTTCTGAA"

If you have additional information for this design, enter it here

Other Design -> Validate a Morpholino Oligo you designed

Enter the sequence of the Morpholino you would like to have validated. Please submit only proposed antisense Morpholino sequences using this page. Do not submit sense RNA sequence here! (NOTE: Gene Tools does not validate that your sequence is properly targeted, only that the oligo sequence itself has no known design errors such as self-complementarities or excessive G content)

Oligo Name *

Sequence (this is your proposed Morpholino sequence) *

If you have additional information for this design, enter it here

Other Design -> 5-mispair Control (not recommended as a specificity control)

Enter a sequence of the antisense Morpholino oligo for which you would like us to design a corresponding 5-base mismatch control.

Name for your 5-base mismatch control oligo *

Sequence of antisense Morpholino oligo *

If you have additional information for this design, enter it here

Other Design -> Other Oligo Design

Enter sequence description and sequence data, then describe what you are looking for in the comments box.

Oligo Name *

Target Description (Where on the sequence is the target you want to block and what sort of process occurs there?) *

Sequence Data *

If you are requesting an oligo in the Other category, you do not want us to use our usual targeting strategies. Please describe in this box what it is that you want the oligo to do.

Leave this field blank

You are here

Gene Tools Oligo Design Form

Customer Information

Translation Blocking Oligo, mRNA Target

Translation Blocking Oligo -> mRNA sequence 5' UTR

Translation Blocking Oligo -> Ensembl mRNA transcript ID

Translation Blocking Oligo -> GenBank mRNA transcript

Splice Modifying Oligo, pre-mRNA Target

Splice Modifying Oligo -> Up to 6 intron-exon or exon-intron boundaries

Splice Modifying Oligo -> Ensembl mRNA transcript ID and target exon number

Target Exon

MicroRNA Inhibiting, miRNA Target

RNA Target Protecting Oligo

Other Design -> Validate a Morpholino Oligo you designed

Other Design -> 5-mispair Control (not recommended as a specificity control)

Other Design -> Other Oligo Design

Note: a red asterisk (*) by a form field indicates a required field.