Table 3.

Overview of Great Gerbil MHCII Genes and Their Location in the Genome Assembly

Gene	Scaffold	Strand	Start	End	Size (aa)	Full-Length Coding Sequence
Rhop-DPB	scaffold00896	−	116,069	105,406	264	Yes
Rhop-DPA	scaffold00896	+	117,514	120,092	252	Yes
Rhop-DOA	scaffold00896	+	125,319	127,406	241	Yesa
Rhop-DMa	scaffold00896	+	166,162	168,926	265	Yesb
Rhop-DMb	scaffold00896	+	175,763	182,090	257	Yes
Rhop-DOB	scaffold00896	+	239,915	245,006	172	Noc
Rhop-DQB	scaffold00896	+	271,007	278,482	231	Nod
Rhop-DQA	scaffold00896	−	294,074	290,301	255	Yes
Rhop-DRB1	scaffold00896	+	310,644	319,368	265	Yes
Rhop-DRB2	scaffold00896	+	326,384	347,931	272	Yese
Rhop-DRA	scaffold00896	−	355,351	351,425	254	Yes
Rhop-DRB3	scaffold00896	−	403,768	395,068	265	Yes

note.—The table details the assigned great gerbil gene names, which scaffold and in what orientation they are located as well as genomic location on the scaffold for start and end of the genes. Information on the size of the translated amino acid sequence and whether it is complete is also shown. In addition, see supplementary figure S7, Supplementary Material online.

^aMissing final residue and stop codon due to conserved overlapping splice site.

^bUnable to locate a stop codon. The structure of the final two exons is conserved among human, mouse, and rat with the ultimate residue overlapping the splice site. The final coding exon therefore only contains 2 bp and the stop codon making it hard to determine the location of the final exon in the gerbil without supporting RNA information.

^cMissing 99 residues (121–219) due to assembly gap.

^dStart location is that of exon 2 as exon 1 is missing due to an assembly gap.

^eThe cytoplasmic tail of β2 genes are encoded by an exon with no known homology to other exons in the MHCII genes and has a low degree of homology between mouse and rat (Monzón-Casanova et al. 2016). There is therefore some uncertainty related to the completeness of the final exon of Rhop-DRB2.