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Frequently asked questions

Mouse


How to find the mouse T cell receptor alpha et beta constant genes sequences to select PCR primer sequences?
Alignments of alleles of the mouse TRAC, and TRBC1 and TRBC2 genes are available in IMGT Repertoire: TRAC, TRBC1, TRBC2
Is there a complete list of the mouse IG and TR genes?
Yes, the complete list of the mouse IG and TR genes, approved by MGI and NCBI Gene, is available at: IMGT Repertoire > 1. Locus and genes > Lists of Mouse (Mus musculus) IG and TR genes, groups, major loci and links between IMGT/GENE-DB, MGI and NCBI Gene. Genes and allele sequences and information can be retrieved from IMGT/GENE-DB.
Why is the mouse TRAJ7 gene considered as an ORF?
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
Only the reading frame codon_start 2 is reported in Alignment of alleles and in Protein displays.
Is there a way to cross-reference the IMGT named TRBV genes with the more common names?
The information is available in IMGT Repertoire
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?
These alignments can be obtained as follows:
  1. query IMGT/GENE-DB
    • Example: Species: Mus musculus, Group: IGHV, Functionality: Functional
    • Do the search.
  2. 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 *).
  3. 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 https://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?
The sequences can be obtained as follows:
  1. query IMGT/GENE-DB
    • Example: Species: Mus musculus, Group: TRAV, Functionality: Functional
    • Do the search.
  2. 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.
  3. Run a ClustalW.
Proceed in the same way for TRBV.
What IMGT genes represent the old Vk21-5 and J558.40?
  • Vk21-5 is a 'constructed' name. The name of the original sequence is 21C (K02161) that corresponds to the germline IGKV3-5*01 gene. https://www.imgt.org/IMGTrepertoire/LocusGenes/genetable/mouse/
  • 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). https://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?
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,
  1. 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).
  2. The germline gene expressed in Vk-Ox1 is encoded by IGHV4-49 (H3 in Even et al. EMBO J. 4, 3439-3445 (1985). https://www.imgt.org/IMGTrepertoire/LocusGenes/genetable/mouse/ The cDNA was previouly sequences by Kaartinen et al. (J. Immunol. 130, 937-945 (1983).
  3. The VHOx-1 is encoded by a gene of the IGHV2 subgroup (previously designated as Q52). https://www.imgt.org/IMGTrepertoire/index.php?section=LocusGenes&repertoire=genetable&species=Mus_musculus&group=IGHV Please note that the nomenclature of the IGHV genes in this table is still provisional but the definitive nomenclature will be available on the IMGT site soon.
For more information, see Correspondence between IGHV nomenclatures
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). https://www.imgt.org/IMGT_vquest/data_releases
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?
  1. For the V-KAPPA domain, go to IMGT Repertoire (IG and TR) > Protein displays: house mouse (Mus musculus) IGKV and identify the IGKV genes with your motif.
  2. Then, query IMGT/GENE-DB
    • Example:
      • Species: Mus musculus
      • Group: IGKV
      • Functionality: Functional
    • Do the search
    • In the result page:
      1. Select genes identified based on your motif in IMGT Protein display,
      2. 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.
  3. 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?
  1. The IMGT reference sequences of mouse IG genes can be retrieved from IMGT/GENE-DB, the IMGT gene database.
    • In the section "IDENTIFICATION", select:
      1. Species: Mus
      2. Molecular component: IG
      3. GeneType: variable
  2. 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".
  3. Please note that: