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I'm trying to get the data for the Human and Mouse 12 and 23 Recomination Signal Sequences (RSS), to run a classification algorithm on it. I'm not a biologist, so I apologise in advance for my misunderstandings and confusion.

A version of the data is available here, but I thought I would try to get it from, if possible. There is also another slightly different version available for the mouse here.

I'm trying to follow the instructions at IMGT-FAQ to obtain Recombination Signal Sequences for the mouse.

Here is what I have selected at the search page:

Species : Mus Musculus
GeneType: any
Functionality: functional
MolecularComponent: any
Clone name: <blank>

IMGT group: IGHV
IMGT subgroup: any
IMGT gene: <blank>

I'm not clear what "Locus", "Main locus", and "IGMT group" mean here exactly. Specifically, what is the difference between "Locus" and "Main locus"?

I think, but am not sure, that IGHV corresponds to V genes in the Immunoglobulin heavy locus (IGH@) on chromosome 14, where locus here denotes collections of genes. Clarifications and corrections appreciated.

I would have expected that the IGH locus would correspond to "IMGT group" entries like "IGHJ, IGHV" etc, and the IGK locus would correspond to IMGT group entries like "IGK, IGKJ, IGKV", but no matter what I select for Locus, it does not change the possible entries for "IMGT group".

Running the search gives

Number of resulting genes : 218 Number of resulting alleles : 350

As instructed, I went to the bottom, selected "Select all genes", clicked on "Choose label(s) for extraction", and selected "V-RS".

I got

Number of results=98

The first few results were

>X02459|IGHV1-4*02|Mus musculus_BALB/c|F|V-RS|395..432|38 nt|NR| | | | 
|38+0=38| | |

>X02064|IGHV1-54*02|Mus musculus|F|V-RS|295..332|38 nt|NR| | | | |38+0=38| 
| |

>M34978|IGHV1-58*02|Mus musculus_A/J|P|V-RS|554..560|7 nt|NR| | | | 
|7+0=7|partial in 3'| |

Ok, now I'm confused. The lengths of the RSS should be 28 or 39. but I counted lengths of 4,7, 31, 38, and 39. Are the results here not supposed to contain the 12 and 23 RSS?

So, I must be misunderstanding things here. Possibly many things. Any explanations and clarifications are appreciated.

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1 Answer 1

I'm not clear what "Locus", "Main locus", and "IGMT group" mean here exactly. Specifically, what is the difference between "Locus" and "Main locus"?

From the same site:

A locus is a set of IG or TR genes that are ordered and are localized in a same chromosomal location, in a given species. […]
A locus comprises the genes of different groups which participate potentially to the synthesis of a polypeptide of the same 'chain type'.

Main locus should have been Locus minus the orphons:

A chromosomal orphon set is a set of IG or TR orphons (genes outside from the main loci) belonging to a same group and localized on the same chromosome in a given species.

However the Main Locus and Locus have the same options; Options for the Locus should have been chromosomes. They must have made a revision in the site but forgot to change the help. I tried setting all the options except any in Locus and selecting all for the Orphons; it yields no result. It works only if you set any in Locus. So it seems Locus option is useless; you can set the Locus as any by default.
For confirmation it is best to ask the authors.

From the changelog:

16 April 2012

  • Update of the IMGT/GENE-DB Query page:

    The search criteria are organized according to the axioms IDENTIFICATION, LOCALIZATION and CLASSIFICATION of IMGT-ONTOLOGY. Addition of new search criteria:

    • MolecularComponent (IDENTIFICATION)
    • Locus (LOCALIZATION): includes main loci and chromosomal orphon sets Main locus: "all" value allows to search genes of all main loci. Chromosomal orphon set: "all" value allows to search genes of all chromosomal orphon sets

For details on the IMGT classification you should refer to this paper.

Fixing a Locus option does not change the IMGT dropdown box option but the results are different. If you try your example and set Main Locus as IGH and IMGT Group as IGKJ you would get no results. It is just a problem of the web interface. Apparently the search works fine.

Running the search

I searched with the exact same criterion as you mentioned and did not get any sequences smaller than 38nt. There must have been some bug which seems to be fixed.

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