Table 2.
Nonsynonymous allelic variants of S and LEW genes located within the chromosome 10 QTL1 BP region.
| Transcript Size (ATG to Stop) | ||||||||
|---|---|---|---|---|---|---|---|---|
| Gene ID | Gene Symbol | Gene Description | Observed S-allele | Observed LEW-allele | Variant RN010 Location | Exon Number | S Rat Variant | LEW Rat Variant |
| 497969 | RGD1559577 | Similar to Riken cDNA 1700020L24 (predicted) | No Product‡ | No Product‡ | 71, 525,070 bp* | 4 | TTC (F326) | TAC (Y326) |
| 303384 | Mmp28 | Matrix metalloproteinase 28 (predicted) | 1577 bp^ | 1577 bp^ | No Variants | - | - | - |
| 287571 | Taf15 | TBP-associated factor 15 (predicted) | No Product‡ | No Product‡ | No Variants | - | - | - |
| 497970 | RGD1559875 | Similar to novel protein (predicted) | No Product‡ | No Product‡ | No Variants | - | - | - |
| 81780 | Ccl5 | Chemokine (C-C motif) ligand 5 | 279 bp | 279 bp | 71 ,61 0,248 bp** | 1 | ATT (114) | GTT (V14) |
| 497971 | LOC497971 | Similar to Ccl9 (predicted) | 354 bp | 354 bp | No Variants | - | - | - |
| 287910 | Ccl6 | Chemokine (C-C motif) ligand 6 | 348 bp | 348 bp | No Variants | - | - | - |
| 25542 | Ccl3 | Chemokine (C-C motif) ligand 3 | 279 bp | 279 bp | No Variants | - | - | - |
| 116637 | Ccl4 | Small inducible cytokine A4 | 279 bp | 279 bp | No Variants | - | - | - |
| 171059 | Expi | Extracellular peptidase inhibitor | 183 bp | 183 bp | No Variants | - | - | - |
| 360228 | LOC360228 | WDNM1 homolog | 192 bp | 192 bp | No Variants | - | - | - |
| 497972 | RGD1566204 | Similar to 2700008B19Rik protein (predicted) | 3759 bp | 3759 bp | No Variants | - | - | - |
| 25640 | Tcf2 | Transcription factor 2 | 1677 bpt†^ | 1677 bp†^ | No Variants | - | - | - |
| 85432 | Ddx52 | ATP-dependent, RNA helicase | 1797 bp | 1797 bp | 72,223,895 bp*** | 2 | AAA (K73) | ACA (T73) |
| 84479 | Ap1gbp1 | AP1 gamma subunit binding protein 1 | 3417 bp†^ | 3417 bp†^ | No Variants | - | - | - |
| 360580 | Dusp14 | Dual specificity phosphate 14 (predicted) | 597 bp^ | 597 bp^ | No Variants | - | - | - |
| 360581 | Tada2l | Transcriptional adapter 2-like | 1332 bp† | 1332 bp† | No Variants | - | - | - |
| 60581 | Acaca | Acetyl-coenzyme A carboxylase alpha | 7038 bp | 7038 bp | No Variants | - | - | - |
Total kidney RNA was used to obtain all the transcripts except for RGD1566204 and Ap1gbp1. A mixed pool of total RNA obtained from S and LEW rat liver, spleen, heart, pancreas, lung, and thyroid was used to obtain the RGD1566204 and Ap1gbp1 transcripts.
Total kidney RNA and the mixed pool of RNA was tried for those few genes that did not give a transcript product. Sequence information for those genes that did not give us a transcript product was obtained by sequencing the genomic DNA. All nonsynonymous variants observed in the amplified transcripts were confirmed by sequencing the genomic DNA.
Chromosomal location is similar to position 12,524,275 of accession number NW_047336 viewed on plus strand;
Chromosomal location is similar to position 12,609,453 of accession numboer NW_047336 viewed on plus strand;
Chromosomal location is similar to position 13,223,100 of accession number NW_047336 viewed on plus strand; The S versus LEW variant nucleotide is underlined; The amino acid and its position within the protein is in parenthesis. Some genes, as designated by †, showed more than one type of transcript variant. All transcript sizes were of expected size, according to NCBI, with some exception as designated by ^. Mmp28 transcript size and sequence was the same as given by NCBI, but Ensembl’s annotation was shorter by seven amino acids at the c-terminal. Tcf2 transcript size and sequence was the same as that given by NCBI, except that the S and LEW transcripts had an additional amino acid (Q403) that the NCBI does not annotate. That amino acid is annotated by Ensembl and is also found in the mouse sequence of this gene’s protein product. Dusp14 transcript obtained was similar to that annotated by Ensembl and overlapped with last segment of the sequence annotated by NCBI. The first 396 bp of the Dusp14 NCBI annotated sequence was confirmed by sequencing the genomic DNA of S and LEW. Ap1gbp1 transcript sequence and size differed from both NCBI’s and Ensembl’s. However, the sequence mostly resembled that of the sequence annotated by Ensembl. Some of the observed transcript variants had sizes and sequences that looked more like a composite between the NCBI and Ensembl deposited sequences for this gene. For all the genes, the gene-specific primers used in amplifying the gene transcripts, genomic DNA amplification, and amplicon sequencing were designed based on the NCBI’s deposited sequences. All S and LEW sequences characterized for these genes were deposited in Genbank with accession numbers ranging from EF121971 to EF122008.