Table 3.
Thirty-Eight Predicted Genes That Were Partially Verified With Primers in the Predicted UTRs but Did Not Become Rat RefSeqs Between Our Experiment and Submission of This Paper
| Rat prediction | AA | Top human nr hit | Accession | AA | %ID | Ortho? | Synt? | dS | HGMD hit if different | Accession | %ID |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Rn21.chr10.25.002 | 443 | GABA receptor α-1 precursor | NP_000797 | 456 | 99 | Yes | Yes | 0.55 | |||
| Rn21.chr7.82.002 | 438 | Exostosin-1 (EXT1) | NP_000118 | 746 | 97 | Yes | Yes | 0.27 | |||
| Rn31.chr3.13.009 | 325 | LIM homeobox TF 1 β (LMX1B) | NP_002307 | 372 | 97 | Yes | Yes | 1.5 | |||
| Rn21.chr12.39.013 | 517 | T-box 5 | NP_000183 | 518 | 96 | Yes | Yes | 1.13 | |||
| Rn21.chr2.176.012 | 747 | TRIFIC | AAP51206 | 759 | 95 | Yes | Yes | 0.46 | Midline 1 | NP_000372 | 24 |
| Rn21.chr4.130.006 | 213 | Microphthalmia-associated TF | NP_000239 | 419 | 94 | Yes | Yes | 0.51 | |||
| Rn31.chr1.200.001 | 572 | Dihydropyrimidinase-like 4 (DPYSL4) | NP_006417 | 572 | 93 | Yes | Yes | 0.93 | Dihydropyramidinase | NP_001376 | 59 |
| Rn31.chr9.15.002 | 188 | G protein-coupled receptor 136 | AAP72128 | 350 | 93 | Yes | Yes | 0.39 | Retinal GPCR | NP_002912 | 28 |
| Rn31.chr14.37.010 | 339 | Sarcoglycan γ (dystrophin-associated) | NP_000223 | 318 | 93 | Yes | Yes | 1.1 | |||
| Rn21.chr1.237.016 | 1090 | Glycine dehydrogenase (GLDC), mitochondrial precursor | NP_000161 | 1020 | 92 | Yes | Yes | 0.83 | |||
| Rn21.chr1.92.009 | 448 | Human Prediction | XP_293343 | 518 | 92 | Yes | Yes | 0.56 | Kell blood group precursor | NP_066569 | 42 |
| Rn21.chr2.93.001 | 439 | Hepatocyte nuclear factor 4 γ chain | NP_004124 | 408 | 91 | Yes | Yes | 1.12 | Hepatocyte nuclear factor 4-α | NP_849180 | 64 |
| Rn31.chr7.105.006 | 447 | N-myc downstream-regulated gene 1 | NP_006087 | 394 | 90 | Yes | Yes | 1.08 | |||
| Rn31.chr8.16.004 | 718 | N-acetylated α-linked acidic dipeptidase 2 | NP_005458 | 740 | 89 | Yes | Yes | 0.59 | Transferrin receptor 2 | NP_003218 | 28 |
| Rn21.chr8.61.011 | 522 | Bardet-Biedl syndrome 4 | NP_149017 | 519 | 88 | Yes | Yes | 0.41 | |||
| Rn31.chr10.56.021 | 1158 | PER1 (circadian pacemaker protein) | NP_002607 | 1290 | 87 | Yes | Yes | 0.49 | PER2 (circadian pacemaker) | NP_073728 | 44 |
| Rn21.chr14.79.012 | 629 | SH3-domain binding protein | NP_003014 | 561 | 86 | Yes | Yes | 0.74 | |||
| Rn31.chr14.38.008 | 398 | TXK tyrosine kinase, PTK4 | NP_003319 | 527 | 86 | Yes | Yes | 0.73 | Bruton tyrosine kinase (BTK) | NP_000052 | 57 |
| Rn31.chr8.49.002 | 247 | Human Prediction | XP_113683 | 235 | 84 | Yes | Yes | 0.55 | Myelin protein zero | NP_000521 | 32 |
| Rn31.chr19.25.027 | 436 | Glutaryl-CoA dehydrogenase | NP_000150 | 438 | 84 | Yes | Yes | 1 | |||
| Rn21.chr1.79.002 | 594 | Glucose phosphate isomerase/neuroleukin | NP_000166 | 558 | 82 | Yes | Yes | 0.85 | |||
| Rn21.chr16.39.002 | 345 | Aspartylglucosaminidase | NP_000018 | 346 | 82 | Yes | Yes | 0.42 | |||
| Rn21.chr1.207.007 | 214 | Iduronate 2-sulphatase (IDS) | NP_000193 | 550 | 81 | No | No | 1.79 | |||
| Rn21.chr17.48.008 | 292 | Na/PO4 cotransporter (SLC17A4) | NP_005486 | 497 | 81 | Yes | Yes | 0.44 | Solute carrier family 17 (anion/sugar transporter), member 5 | NP_036566 | 46 |
| Rn21.chr5.183.007 | 760 | 5,10-methylenetetrahydrofolate reductase (NADPH) | NP_005948 | 656 | 80 | Yes | Yes | 0.92 | |||
| Rn21.chr2.29.005 | 590 | Methylcrotonoyl-co-A carboxylase 2 β | NP_071415 | 563 | 79 | Yes | Yes | 0.57 | |||
| Rn31.chr5.154.011 | 548 | Selenoprotein N, 1 | NP_065184 | 590 | 79 | Yes | Yes | 1.02 | |||
| Rn21.chr7.4.031 | 542 | Lamin B2 (LMNB2) | NP_116126 | 600 | 78 | Yes | Yes | 2.17 | Lamin A/C | NP_005563 | 52 |
| Rn21.chr8.26.002 | 590 | Putative β-galactosidase (hypothetical) | NP_612351 | 636 | 78 | Yes | Yes | 0.6 | Galactosidase β | NP_000395 | 38 |
| Rn21.chr4.114.014 | 254 | Deoxyguanosine kinase isoform a precursor | NP_550438 | 277 | 78 | Yes | Yes | 0.48 | Thymidine kinase 2, mitochondrial | NP_004605 | 33 |
| Rn21.chr8.69.013 | 143 | Tropomyosin—human (fragment) | T08796 | 308 | 76 | No | No | 3.24 | Tropomyosin 1α | NP_000357 | 65 |
| Rn21.chr16.59.012 | 208 | Werner syndrome protein (WRN) | NP_000544 | 1432 | 74 | Yes | Yes | 0.56 | |||
| Rn31.chr4.182.011 | 107 | Nucleoside phosphorylase (NP) | NP_000261 | 289 | 71 | No | No | 0.62 | |||
| Rn21.chr14.17.012 | 338 | Methylene tetrahydrofolate dehydrogenase 2 precursor (MTHFD2) | NP_006627 | 344 | 70 | No | No | 2.06 | Methylenetetrahydrofolate dehydrogenase | NP_005947 | 40 |
| Rn31.chr11.32.006 | 213 | Interferon γ receptor 2 (IFNGR2) | NP_005525 | 337 | 68 | Yes | Yes | 0.67 | |||
| Rn31.chr3.4.041 | 311 | Glycosyltransferase family 6 like | NP_892019 | 308 | 63 | Yes | Yes | 1.34 | ABO blood group (ABO glycosyl transferase) | NP_065202 | 39 |
| Rn31.chr3.5.015 | 351 | Lysophosphatidic acid acyltransferase | NP_006403 | 278 | 59 | Yes | Yes | 1.63 | |||
| Rn31.chr4.29.008 | 159 | Lipoprotein-associated coagulation inhibitor (TFPI) | NP_006278 | 304 | 36 | No | No | 3.41 |
We determined whether the prediction is a probable ortholog of the top human hit by considering whether there is conserved synteny around the pair (Synt?) and what the estimated neutral substitution rate is since their nearest common ancestor (dS). The %ID column shows the percentage identity of the highest-scoring HSP returned when NCBI's program Blast2Sequences (bl2seq) is applied to the predicted and RefSeq proteins.