The mouse TRAJ7 gene is an ORF according to the IMGT Scientific chart rules for the description of
functionality.
Indeed, it has indeed an open reading frame (and even two! both ORF, as discussed below).
The functionality of the germline TRAJ genes is reported in
"Germline gene table: Mouse
(Mus musculus) TRAJ".
If, following the TRAV-J rearrangement, the translation of the TRAJ7 is in the reading frame
"codon_start 2":
the reading frame is similar to that observed for the human TRAJ7.
The DONOR-SPLICE is all right, however the conserved Phenylalanine (F) of the classical J-REGION motif F - G - X - G is replaced by a Leucine (L). It is the reason why the mouse germline TRAJ7 gene is not considered as a functional gene but as an ORF.
Mus D Y S N N R L T L G K G T Q V V V L P
M64239,TRAJ7*01 G GAC TAC AGC AAC AAC AGA CTT ACT TTG GGG AAG GGA ACC CAG GTG GTG GTG TTA CCA A
Human D Y G N N R L A F G K G N Q V V V I P
M94081,TRAJ7*01 T GAC TAT GGG AAC AAC AGA CTC GCT TTT GGG AAG GGG AAC CAA GTG GTG GTC ATA CCA A
What is interesting is that, if following the TRAV-J rearrangement, the translation of the TRAJ7 is in the reading frame
"codon_start 1", the translation would display a classical and conserved J-REGION motif F - G - X - G at the right place, but the DONOR-SPLICE will be, in that case, defective ("nngt" instead of "ngt", with splicing occurring before "g" in both cases). That means that the J-REGION cannot be spliced to the TRAC gene. The sequence will be "unproductive" (for a rearranged sequence, the functionality is either "productive" or "unproductive").
Reading frame "codon_start 1"
Mus G L Q Q Q Q T Y F G E G N P G G G V T
M64239,TRAJ7*01 GGA CTA CAG CAA CAA CAG ACT TAC TTT GGG GAA GGG AAC CCA GGT GGT GGT GTT ACC AA
In each case, the query can be done by an automatic search on the page with the common name.
Another more general way is to make a search by Google on the IMGT site (available at the IMGT Home page).
How to get alignments of parts of the mouse germline V genes in order to design subgroup specific primers for PCR amplification of the V gene repertoire?
In the result page:
Select all genes
then at the bottom of the page in: IMGT label extraction from IMGT/LIGM-DB reference sequences
Choose label(s) for extraction
For instance FR1-IMGT.
Note that you can make more sophisticated queries by choosing for instance L-PART2, with the option
Nucleotide sequences
(option: add nucleotides in 5' and in 3'*)
which will give you L-PART2 + the 24 first nucleotides of the FR1-IMGT
however be aware that sequences which are partial and do not contain the label L-PART2 will be missed
in that query (as indicated in the note *).
Run a ClustalW.
Is it possible to use IMGT/V-QUEST for the analysis of TRB D-J junctions?
Yes, it is possible to use IMGT/V-QUEST for analysis of TRB D-J junctions.
Here are the different steps:
identify and delete from your sequences the 'germline' part upstream of the D-REGION, that is, for example,
the sequence that ends with AGCTGTAACATTGTG for mouse TRB D-J sequences
copy the sequences in IMGT/V-QUEST
add for each sequence the variable region of a given TRBV (the same one for all your sequences).
Any functional TRBV from the IMGT/V-QUEST reference directory can be used.
Select 'Synthesis view' in choosing only 'Results of IMGT/JunctionAnalysis'
as a display (uncheck the other display boxes).
What is the difference in the gene content between IMGT Gene table and IMGT reference directory?
The IMGT Gene table, for instance, the IMGT Gene table Mouse (Mus musculus) IGHV provides:
the accession numbers from which the IMGT reference directory sequences were extracted ('Accession numbers')
the accession numbers of identical sequences found once genes and alleles have already been identified ('Sequences from the literature').
This distinction is also found in IMGT/GENE-DB (same content as IMGT Gene table, except for the notes).
'Sequences from the literature' are nomust included in the 'IMGT reference directory'.
This allows to avoid redundancy and to have only one sequence per allele of each gene.
The query http://www.imgt.org/genedb/GENElect?query=7.5+IGHV&species=Mus+musculus
gives access to the complete 'IMGT reference directory'
for the Mus musculus genes and alleles (with one sequence per allele). All the mouse IGHV genes are present in the IMGT reference directory,
with all their alleles (indicated by an asterisk followed by numbers). If different mouse strains have the same allele, there is only one sequence in the IMGT reference directory.
Note that IMGT sequences are identified with accession numbers, gene and allele name, species and strain if known.
How to obtain sequences for the design of primers to identify mouse TR alpha and beta genes in mouse T cells?
in the result page:
Select all genes
then at the bottom of the page in: IMGT label extraction from IMGT/LIGM-DB reference sequences
Choose label(s) for extraction
For instance: L-PART1.
Run a ClustalW.
Proceed in the same way for TRBV.
What IMGT genes represent the old Vk21-5 and J558.40?
J558.40 (AF303871) is a cDNA from BALB/cByJ with a 96.88 % identity (at the nucleotide level) with the IGHV1-69*02 gene. It is not a germline gene (this is a frequent error in the literature for mouse genes).
I suppose your question is related to a paper by Boiers U. et al. in Eur. J. Immunol. 38, 2784-2795 (2008).
If so, you might be interested to know that the anti-collagen CIIC1 Fab (from DBA/1 mouse), that has been crystallized,
is available in IMGT/3Dstructure-DB (2vl5).
http://www.imgt.org/3Dstructure-DB/cgi/details.cgi?pdbcode=2VL5.
It shows that, at the amino acid level, the closest V regions of CIIC1 are IGHV1-61*01 (90.80%) et IGKV3-5*01 (97%).
The low percentage of identity for the IGHV gene is not surprising as the DBA/1 germline genes are not yet sequenced.
What do the D and /DV in the mouse TRA genes mean?
The /DV added in the gene name after the TRAV gene symbol means that the mouse TRAV gene has been found rearranged not only to TRAJ genes, but also to TRDD and TRDJ genes.
Ex: TRAV15-1/DV6-1
For more information see the publication:
Bosc, N. and Lefranc, M.-P., "IMGT Locus in Focus: The mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes", Dev. Comp. Immunol., 27, 465-497 (2003).
PMID: 12697305
What is the IMGT® gene match for TEPC15 and VkOx1?
TEPC15, VkOx1,.. refer to clone or antibody designations which were identified by their different idiotypes and were shown to be specific of different haptens (phosphorylcholine (PC), oxazolone (Ox), etc.).
This has been widely extrapolated in the literature, and the same designations have been used for antibodies sharing the same idiotypes and specificities than the original ones. If the sequences of these antibodies are in the generalist databases, it is possible to identify the genes used by these antibodies. However, these designations cannot be used for germline gene names.
For examples,
TEPC15 is an antibody with an anti-PC specificity, expressed by an IgA myeloma. The variable domain is encoded
by the a V gene belonging to the IGHV7 subgroup (previously designated as S107).
The germline gene expressed in Vk-Ox1 is encoded by IGHV4-49 (H3 in Even et al. EMBO J. 4, 3439-3445 (1985).
http://www.imgt.org/IMGTrepertoire/LocusGenes/genetable/mouse/
The cDNA was previouly sequences by Kaartinen et al. (J. Immunol. 130, 937-945 (1983).
Why is it possible to find identical IMGT names for different genes?
The IMGT-ONTOLOGY concepts of classification assign gene and allele names inside a given species.
It means that you may find identical or different allele sequences between different strains of a same species (without bothering about the species name).
In contrast, if you compare sequences of different species, you need to always associate the genus and species to the gene and allele name.
For example:
M15520 is Mus musculus IGKV10-96*01
AF441451 is Mus spretus IGKV10-96*01
In tools, IMGT uses an abbreviation of 6 letters (3 for the genus and 3 for the species), for instance: Musmus for Mus musculus, Musspr for Mus spretus).
IMGT/V-QUEST has been upgraded to display these abbreviations for mouse, teleostei and chondrichthyes sequences since Release 201030-3 (28th of July 2010).
http://www.imgt.org/IMGT_vquest/share/textes/datareleases.html
In the results display you will see, for example: Musmus IGKV10-96*01, Musspr IGKV10-96*01.
How to design V primers to sequence a monoclonal antibody Fab for which only partial V domain amino acid sequences (motifs) are known?
Select genes identified based on your motif in IMGT Protein display,
then at the bottom of the page in: IMGT label extraction from
IMGT/LIGM-DB reference sequences, Choose label(s) for extraction.
For instance L-PART1+L-PART2.
Run a ClustalW.
The same procedure can be followed for the VH.
How to download the amino acid sequences (in fasta format) of the IG variable regions from mouse?
The IMGT reference sequences of mouse IG genes can be retrieved from IMGT/GENE-DB, the IMGT gene database.
In the section "IDENTIFICATION", select:
Species: Mus
Molecular component: IG
GeneType: variable
The results page displays the list of selected genes.
At the bottom of the page you may select all genes.
In order to get the amino acid sequences in FASTA format, select
"F+ORF+in-frame P amino acid sequences" or "F+ORF+in-frame P amino acid sequences with IMGT gaps"
in the column "IMGT/GENE-DB allele reference sequences in FASTA format".
Please note that:
the GENE-DB reference sequences in FASTA format for IG and TR genes are also available from the IMGT download
