File S2 - Predicted location of RNF212 on the Sheep genome Oar_v3.1
The locus RNF212 has not been annotated on the domestic sheep genome (Oar_v3.1). Here,
we present evidence that RNF212 occurs within the region most highly associated with
autosomal crossover count (ACC). Sheep sequences for RNF212 were obtained from
Genbank (Accession Numbers provided in Figure 1 and aligned against the Oar_v3.1 genome
sequence using BLAST v2.2.27+ using the default parameters and a word size of 15 to
determine if the locus was likely to be present within this region. Matches of length < 50 bp
and matching bases of < 95% were discarded .The strongest associations on the assembled
genome sequence were at the sub-telomeric region of chromosome 6 identified in the main
results, falling between positions 116,427,802 and 116,446,904 (Figure 1). This positioned
RNF212 between an uncharacterised protein (orthologous to Tmed11) and FGFRL1, and
suggested that its lack of annotation on the domestic sheep genome is due to its occurrence
across a gap in contiguous sequences (Figure 2). Gene order in this region showed high
similarity to gene orders obtained for homologous genome regions in cow (UMD3.1), dog
(CanFam3.1), human (GRCh38) and mouse (GRCm38); all annotations were obtained from
Ensembl build v1.79 (Cunningham et al. 2014). The alignment of RNF212 shown in Figure 5
(main text) and Figure 2 is to sequence XM_012167676.1.
References
Cunningham F., Amode M. R., Barrell D., Beal K., Billis K., Brent S., Carvalho-Silva D.,
Clapham P., Coates G., Fitzgerald S., Gil L., Giron C. G., Gordon L., Hourlier T., Hunt S. E.,
Janacek S. H., Johnson N., Juettemann T., Kahari a. K., Keenan S., Martin F. J., Maurel
T., McLaren W., Murphy D. N., Nag R., Overduin B., Parker a., Patricio M., Perry E.,
Pignatelli M., Riat H. S., Sheppard D., Taylor K., Thormann a., Vullo a., Wilder S. P.,
Zadissa a., Aken B. L., Birney E., Harrow J., Kinsella R., Muffato M., Ruffier M., Searle S.
M. J., Spudich G., Trevanion S. J., Yates a., Zerbino D. R., Flicek P., 2014 Ensembl 2015.
Nucleic Acids Res. 43: D662–D669.
Fig 1. Alignments of 23 Ovis RNF212 nucleotide sequences (obtained from Genbank) against
the sub-telomeric regions of Oar_v3.1 chromosome 6. Genbank IDs for each sequence are
given on the left axis. The color indicates the percentage sequence match for each segment
of aligned sequence.
Fig 2. Putative positioning of RNF212 (Accession XM_012167676.2) against the subtelomeric region of Oar_v3.1 chromosome 6. The tiling path in green indicates the
contiguous sequence that contributes to the genome sequence used in this study. Other
annotated loci within this area are indicated in the segment above the putative RNF212
position. Figure obtained using the NCBI Genome Viewer (http://www.ncbi.nlm.nih.gov/)