Online supplemental material, Cort, et al.
Contains three supplemental figures and a table of primers used in this report.
Supplemental Figure 1. This figure shows the imputed protein sequences of UBD from 11 inbred strains of rats. Underlined amino acids distinguish the haplotypes. The B2-SINE element is found in the promoter of the L haplotype (see text).
Supplemental Figure 2. Construction of two Ubd promoter-reporter plasmids. The indicated amplicons (containing the microsatellite region or the more proximal promoter region) were separately inserted into the pGL3 luciferase vector and used for expression comparisons.
Supplemental Figure 3. This figure shows a portion of the nucleotide sequence of the 5’ end of the Ubd gene in LEW.1W, LEW.1WR1, and LEW.1WR1-UBD-KO rats, with the targeted mutation indicated by dashes. Underlined nucleotide is a non-synonymous polymorphism between LEW.1W and LEW.1WR1.
Supplemental Figure 1
A HAPLOTYPE (LEW.1WR1, LEW.RT1a, PVG.R8, PVG.RT1u)
MASCVCVVRSEQWPLMTFDTTMSDKVKKINEHIRSQTKVSVQDQILLLDSKILKPHRALSSYGIDKENTIHLTLKVVKPSDEELPLSLVESGDEGQRHLLRVRRSSSVAQVKEMIENVTAVPPKKQIVNCNGKRLEDGKIMADYHIKSGSLLFLTAHCIGG
BB HAPLOTYPE (BBDP, BBDR, PVG.R23)
MASCVCVVRSEQWPLMTFDTTMSDKVKKINEHIRSQTKVSVQDQILLLDSKILKPHRALSSYGIDKENTIHLTLKVVKPSDEELPLSLVESGDEGQRHLLRVRRSSSVAQVKEMIENVTAVPPKKQIVNCNGKRLEDGKIMADYNIKSGSLLFLTAHCIGG
L HAPLOTYPE (WF, LEW.1W, LEW, KDP)(All have SINE element in Ubd promoter)
MASCVCVVHSEQWPLMTFDTTMSDKVKKINEHIRSQTKVSVQDQILLLDSKILKPHRALSSYGIDKENTIHLTLKVVKPSDEELPLSLVESGDEGQRHLLRVRRSSSVAQVKEMIENVTAVPPKKQIVNCNGKRLEDGKIMADYNIKSGSLLFLTAHCIGG
Supplemental Figure 2
Supplemental Figure 3
.
Supplemental Table 1. Ubd gene-specific primersused on genomic DNA to amplify the region by PCR
Forward primer (5'-3') / Reverse primer (5'-3')Ubd 5’ promoter / GGGAAAGCATGATCAAGGAA / CAGAGGCCGAGTGAGAAAAG
Ubd sequencing 5' (set1) / GGAATCCTTGAGAGCAAAGG / CAGTGGAGGTTTTTGCCCTA
Ubd sequencing 5' (set2) / GGGTCAGGTTGGGAAATGTA / GCCTCATGAAGCACAATGTC
Ubd sequencing intron (set1) / CTTTTCTCACTCGGCCTCTG / TATGGGGCTTGAGGATCTTG
Ubd sequencing intron (set2) / TAGGGCAAAAACCTCCACTG / TATGGGGCTTGAGGATCTTG
Ubd sequencing intron (set3) / AATATGCAGGACCAGGGCTA / TAGGTTTGTGATGCCACAGG
Ubd sequencing 3' / ACGGGCATTCTCTGATGACT / TCCACCCCACTTCAAATCTT
Ubd sequencing 3' (set2) / GTTGTTGGGAAGGAACTGGA / GAAACAAAGAATCATAAAACTGGACA
Ubd 3’UTR and beyond (F) / AAGATTTGAAGTGGGGTGGA / GTGTGGTCATCCTGTTGGTG
Ubd 3'UTR new seq / AAGATTTGAAGTGGGGTGGA / CCTGCACACACCCATGTACT
Ubd promoter cloning / CAAGGTACCCTCCCCTTCAT / AGTCAGAGCTCGAGTGAGAA
Ubd-ZFN / CCTGTGGCATCACAAACCTA / TATGGGGCTTGAGGATCTTG
RT1-N1 3' microsatellite / GTTTCCCTGTGGCTTTCAGA / CTGTGGAGACGGAGGAGAAG
Ubd realtime / CTTTTCTCACTCGGCCTCTG / GAGACCTTGGTTTGGGACCT
RT1-N1 / RT1-N2 realtime / GAGCTGCTGCAGAAATACCC / CAGGGTGACATCACCTTCAG
Nrm realtime / GCTTTGTCCTCCACGTTGTT / TAGAGCCCGAGGAGACTTCA
Lta realtime / CTGCTGGCCCTGCCTCTA / TGAATTCTGTTTGCTGGGGTA
Ltb realtime / GGGGGAACCAGAAACTGACT / TCAGAAACGCTTCTTCTTGG
Tnf realtime / GCTCCCTCTCATCAGTTCCA / GCTTGGTGGTTTGCTACGAC
Lst1 realtime / TCCTGCTTGTCATCATCCTG / TGCCTTCCATATCACTGCTG
Vars realtime / GCTCCTGCTAGCCTCTGTGT / TCCGGGTCAGGTTGTAGTCT
Neu1 realtime / TCCGGCATTGTCTTCTTCTC / GCTGTCAGGGATGAGTAGCC