ABG: Germline gene directories of mouse

Index


Aim of these directories

VH and Vk Directories description

VH and Vk Multiple alignments description

Directories summary



Aim of these directories

The knowledge about the number and diversity of the V germline genes repertoire is a key to understand the origin, structure and function of antibody molecules. This learning is, in turn, a very important starting point to address questions about the V gene usage under physiological conditions as well as in pathological disorders of the immune system.

The best studied species regarding antibody structures and sequences are humans and mice. In the former, the knowledge about the number of V germline genes and sequences has been recently completed (V BASE). However, in mice this information remains currently incomplete.

The immune system of the mouse has been the subject of decades of intensive investigation and thus, it is reasonable to suppose that a large amount of its V germline genes have been described today. Nonetheless, the access to this information is very difficult due to the enormous amount of information and sequences accumulated in databases as well as in literature.

To facilitate the access to this information and thus have a proper estimation of the mice V germline gene repertoire, here we offer a directory of the mouse VH and VK germline segments. The sequences were obtained by searching the Mus musculus VH and Vk genes reported as germline genes or pseudogene sequences in Genbank, LIGM as well as in the literature (last update on April, 1996 and december, 1996, respectively). Starting form this raw material, we then analyze the sequences and made a multiple amino acid sequences VH alignment and Vk alignment with those unique (non-redundant) V genes having reported the hypervariable loops.


VH Directory description

In order to make a proper estimation of the V germline genes repertoire in mice (Mus musculus), a directory of VH gene segments was built from sequences files originally obtained from current literature on the subject and databases such as Genbank and LIMG as well. All entries herein shown were given format according to Genbank standards although those taken from the literary sources might not be - up to the best of the authors knowledge - contained in any public access database.

The directory is shown in a table format subdivided in the following way:

Germlines: It includes all sequences reported as potential functional genes with at least both CDR1 and CDR2. Sequences without either one of them were taken as fragments and were not included in this group. Pseudogenes: It gathers all sequences reported as pseudogenes or sequences whose formal translation displays them as interrupted by termination codons in the variable exon. Others: It encompasses all germline genes and pseudogenes entries corresponding to fragments or those pseudogenes whose formal translation does not allow the reconstruction of an Ig-like sequence.

The description of each directory column is:


Vk Directory description

In order to make a proper estimation of the V germline genes repertoire in mice (Mus musculus), a directory of Vk gene segments was built from sequences files originally obtained from current literature on the subject and databases such as Genbank and LIMG as well. All entries herein shown were given format according to Genbank standards although those taken from the literary sources might not be - up to the best of the authors knowledge - contained in any public access database.

The directory is shown in a table format subdivided in the following way:

Germlines: It includes all sequences reported as potential functional genes with at least both CDR1 and CDR2. Sequences without either one of them were taken as fragments and were not included in this group. Pseudogenes: It gathers all sequences reported as pseudogenes or sequences whose formal translation displays them as interrupted by termination codons in the variable exon. Others: It encompasses all pseudogenes entries corresponding to those pseudogenes whose formal translation does not allow the reconstruction of a normal sequence.

The description of each directory column is:


VH Multiple alignment description

In order to have a representative sample of the VH mice repertoire, our initial database gathered the VH gene sequences as reported in current literature and the GenBank and LIGM databases. This information was processed to discard those sequences that were duplicated or were different by only two nucleotides without change of amino acids in the coding region. These sequences are indicated in the alignment by their different gene segment names (Name, clone or sequence accenssion number in Genbank) separated by a slash. The sequences are sorted and aligned according to the differences comprised in region CDR1-FR2-CDR2, which is common to all of them.

In the alignment:

The multiple sequences alignments and all calculations therein presented were performed using the VIR package (Almagro et al., Biosystems 35: 25-32, 1995). A more wide discussion of the procedures here used to obtain the sequences is given in: Almagro et al., Mol. Immunol. 34: 1199-1214, 1997.

Vk Multiple alignment description

As in VH, in order to have a representative sample of the Vk gene sequences we search all the information on Vk germlines of the mouse in current literature, GenBank and LiGM databases. This information was processed to discard those sequences that were duplicated or were different by only two nucleotides without change of amino acids in the coding region. These sequences are indicated in the alignment by their different gene segment names (Name, clone or sequence accenssion number in Genbank) separated by a slash.

The rest of them were sorted and aligned to each VK family.

In the alignment:

The multiple sequences alignments and all calculations therein presented were performed using the VIR package (Almagro et al., Biosystems 35: 25-32, 1995). A more wide discussion of the procedures here used to obtain the sequences is given in: Almagro et al. Immunogenetics 47: 355-363, 1998.



Directories summary

VH

Number of entries

germline genes (potentially functional)

213

Pseudogenes (non-functional)

54

Others (Sequences' fragment)

28

Total

295

Fully identical sequences at amino acid level (germline or pseudogene sequences)

68

Sequences in the alignment [(germline + Pseudogenes) - Fully identical]

185








VK

Number of entries

germline genes (potentially functional)

65

Pseudogenes (non-functional)

24

Others (pseudogenes without reconstruction)

8

Total

97

Fully identical sequences at amino acid level (germline or pseudogene sequences)

22

Sequences in the alignment [(germline + Pseudogenes) - Fully identical]

67





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