PMC

Dot-plot matrix of sheep/human TRA/TRD genomic comparison. Using the Pip-Maker program the entire sheep TRA/TRD locus (horizontal axis, positions 22731677 to 22831677 of the reference sequence NC_0194641) (a) or just the TR V region (horizontal axis, positions 22731677 to 22732377 to of the reference sequence NC_0194641) (b) have been plotted against the human counterparts (vertical axes, positions 21621904 to 22552132 in (a) and positions 21621904 to 21622706 in (b) of NC_000014). The transcriptional orientation of each gene is indicated by arrows and arrowheads. Coloured rectangles enclose TR V duplicated regions as referred in the text

CDR3 nucleotide and predicted AA sequences retrieved from the TRA cDNA clones. CDR3-IMGT sequences are shown from codon 105 (codon after the 2nd-Cys 104 of the V-REGION) to codon 117 (codon before J-PHE 118 of the J-REGION) according to the IMGT unique numbering []. Nucleotides of the 3’V-REGION and of the 5’J-REGION are indicated in lower cases. Nucleotides that cannot be attributed to any V or J regions (N-nucleotides) are indicated in capital letters. Numbers in the left and right columns indicate the number of nt that are trimmed from the 3’V-REGION and 5’J-REGION, respectively. The name of the clones and the TRAJ genes is reported

Sheep (Ovis aries) TRA/TRD locus. Schematic representation of the genomic organisation of the sheep TRA/TRD locus on chromosome 7 as deduced from the genome assembly Oar_v3.1. The unplaced genomic scaffolds NW_004080312, NW_004084646 and NW_004084647 are inserted in the map in a potential localization (see text). The diagram shows the position of all related and no-related TRA/TRD genes according to nomenclature. Boxes representing genes are not to scale. Exons are not shown. Arrows indicate transcriptional orientation of the V genes. The arrow above the line of the TRAJ genes indicates the 80 kb region that has been magnified in the lower part of the figure

TRD genes. In a, the IMGT Protein display of the sheep TRDV genes. Only functional genes, ORF and in-frame pseudogenes are shown. The description of the strands and loops and of the FR-IMGT and CDR-IMGT is according to the IMGT unique numbering for V-REGION []. The CDR-IMGT AA lengths are indicated in square brackets. nd: not defined (indicates that the AA sequence of the TRDV1S6 gene is incomplete and its functionality cannot be defined). In b and c, nucleotide and deduced AA sequences of the sheep TRDD and TRDJ genes. The consensus sequences of the heptamer and nonamer [] are provided at the top of the figure and underlined. The numbering adopted for the gene classification is reported on the left of each gene. In b, the AA sequences of the TRDD genes in the three coding frames are reported. In c, the donor splice site for each TRDJ is shown. The canonical FGXG motifs are underlined. The unusual TRDJ1-4 gene motif is in italics. In d, IMGT Protein display of the TRDC gene. Description of the strands and loops is according to the IMGT unique numbering for C-DOMAIN []

CDR3 nucleotide and predicted AA sequences retrieved from the TRD cDNA clones. The first column reports the accession numbers of all cDNA sequences. CDR3-IMGT sequences are shown from codon 105 (codon after the 2nd-Cys 104 of the V-REGION) to codon 117 (codon before J-PHE 118 of the J-REGION) according to the IMGT unique numbering []. They are grouped on the basis of the absence or the presence of one, two, three and four TRDD genes. Nucleotides of the 3’V-REGION and of the 5’J-REGION are indicated in lower cases. The sequences considered to present recognisable TRDD genes are indicated in bold upper cases with the indication of the TRDD gene name. Nucleotide substitutions with respect to the germline TRDD sequence are indicated in bold lower cases. Nucleotides that cannot be attributed to any V, D or J regions (N-nucleotides) are indicated in capital letters on the left and on the right side, and in between of the TRDD regions. Numbers in the left and right columns indicate the number of nt that are trimmed from the 3’V-REGION and 5’J-REGION, respectively. The last column on the right indicates the TRDJ genes