|
Before searching for TILLING mutants, please read each
section so that you will understand how the data is
organized on each site.
General Information:
The user has a 180-day confidentiality period that
begins once s/he is notified by email that there are
TILLING mutations for the gene target. After 180 days,
the TILLING mutant data will be available from our website,
the TILLING Results search page and MaizeGDB as described
below. However, we will not release the name of the
person initiating the request.
We keep track of the TILLING data by "order name"
and this can lead to confusion with respect to what
gene is being TILLed. The order name is a string of
2-8 letters and/or numbers that is unique in our database.
The names that the users give their TILLING targets
do not always reflect the name of the gene being TILLed
for several reasons. First of all, many users have used
"zm" at the beginning of the order name to
reflect that the gene target is from zea mays, but this
would make it harder to search by gene name even if
the user chose to include it in the order name. Also,
some TILLING requests correspond to targets that are
"predicted genes" that have not been characterized
or described. Finally, there are just some order names
that do not give any hint as to the actual gene target
being TILLed.
We struggled with finding
a good way to submit the B73 and W22 sequences for each
TILLING order to GenBank in a way that would avoid confusion
about what gene sequence was being analyzed. We decided
to assign a generic identifier to each sequence that
indicates it is a gene fragment from the Maize TILLING
Project. The identifier is: MTP_inbred_#### (ex. MTP_B73_0006)
where MTP denotes Maize TILLING Project, inbred will
be either B73 or W22, and #### will correspond to a
4 digit number unique to each order. Please note
that on the MaizeGDB website, the identifier has been
abbreviated to: mtp#### (ex. mtp0006).
Maize TILLING Project's Website
We have listed the TILLING
results in a table by the following fields: 1) TILLING
order, 2) BLASTX hit, 3) MTP identifier for B73 and
GenBank Accession number, 4) MTP identifier for W22
and GenBank Accession number, 5) MaizeGDB identifier,
6) number of non-silent mutations in B73 and 7) number
of non-silent mutations in W22.
We have included links to the records on the TILLING
Results and MaizeGDB websites. These records will have
the details regarding the base and amino acid changes
in the mutant and if the mutation is predicted to affect
protein activity as well as the primers sequences used
for TILLING. We have also included links to the GenBank
records so that you can download the B73 and W22 sequence
for each target. Please let us know if there is any
other information that you would like us to display.
TILLING Results Search page
The TILLING
Results Search page is searchable by the DNA or
protein sequence. The TILLING Results record will list
the publicly available TILLING mutants, the SIFT
and PARSESNPs
data as well a link for ordering seed stocks. These
pages are updated automatically when mutations can be
released into the public databases.
MaizeGDB
The Maize TILLING data
is now integrated into MaizeGDB. After 180 days, the
TILLING data are released into publicly accessible sites,
including the STP
searchable database searchable using DNA or protein
sequence), our website [link to chart], MaizeGDB and
GenBank.
We do, however, keep confidential the name of the person
who initiated the request. We will do data transfers
to MaizeGDB approximately every 3 months, but the information
on our website and the STP TILLING Results site will
be current.
When deciding how to display
the TILLING data on MaizeGDB we did not want the order
name to be mistaken for the gene name. To avoid that
confusion, we have decided to list the TILLING targets
by the abbreviated identifier. In the MaizeGDB record
we have included the best hit from the BLASTX search
to facilitate people finding more information about
each TILLING target. The TILLed genes are listed on
MaizeGDB here.
If you click on one of the records (ex. mtp0006)
you will see the following information:
- Primer sequences
- Variations or the TILLING mutations discovered
- Link to the gDNA sequences on GenBank
- Link to related loci (based on BLAST search of the encoded
protein)
If you click on the
variations
link you will see a list of the mutations found
and click on each record to get the seed stock information
(ex mtp0006-W22_c314t)
and also a link to the mutation record in the STP
database which contains the PARSENPS and SIFT reports
and also a web-based form for requesting for seed stocks.
GenBank
The B73 and W22 sequence
for the TILLed fragment and the primers will be deposited
into GenBank.
The sequences deposited in GenBank will have a generic
header: "MTP_Inbred_order number" (i.e. MTP_B73_0015,
MTP_W22_0015).
For the GenBank entry, we decided not to provide a
gene name or gene product for several reasons. First,
the name of the TILLING order name does not necessarily
refer to the name of the gene being TILLed and might
be a source of confusion. Second, some TILLING orders
correspond to a gene fragment and not the entire coding
region. When the TILLING fragment is used in a BLAST
search many hits are returned that are very similar
to each other, and it is difficult to determine which
is the "best hit". Finally, several of the
gene targets TILLed correspond to "hypothetical"
proteins, thus a definitive identification cannot be
given.
|