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Table 2 Re-analysis of genes claimed to be newly discovered human horizontal gene transfers (HGT) in the Crisp et al. [1] study

From: Horizontal gene transfer is not a hallmark of the human genome

Gene ID Gene name Results from Crisp et al. [1] study Results from this study
HGT index Source HGT taxon Best non-chordate metazoan match Bit score Best non-chordate metazoan match Matching protein ID Bit score New HGT index
ENSG00000070269 C14orf101 337 Protist B4LPG6 37 Lingula anatina XP_013409033 566 –192
ENSG00000102805 Ceroid-lipofuscinosis, neuronal 5 84 Protist E3MZU2 39 Lottia gigantea XP_009059770 338 –215
ENSG00000116721 PRAME family member 1 72 Protista A8MVS2 44 No hits    
ENSG00000157358 PRAME family member 15 45 Protista F1SUY5 89 No hits    
ENSG00000232423 PRAME family member 6 45 Protista F1SUY5 92 No hits    
ENSG00000117115, ENSG00000142619, ENSG00000142623, ENSG00000159339 Protein-arginine deiminase, types 2,3,1,5 464 Bacteria B4JS81 45 Priapulus caudatus XP_014670176 560 –51
ENSG00000125458 5′,3′-nucleotidase, cytosolic 135 Bacteria E3LP71 39 Saccoglossus kowalevskii XP_006825056 222 –48
ENSG00000205309 5′,3′-nucleotidase, mitochondrial 108 Bacteria B5DJB4 41 L. anatina XP_013404549 237 –88
ENSG00000133561, ENSG00000133574, ENSG00000179144, ENSG00000196329, ENSG00000213203 GTPase, IMAP family members 6, 4, 7, 5, and 1 51 Plant F1QNI4 94 Crassostrea gigas XP_011437597 208 –63
ENSG00000136153 LIM domain 7 47 Protist H9JLZ2 86 S. kowalevskii XP_006813620 268 –135
ENSG00000136830 Family with sequence similarity 129, member B 74 Protist G6DB46 44 Acropora digitifera XP_015774462 115 3
ENSG00000140718 Fat mass and obesity associated 97 Plant C9J4C3 92 S. kowalevskii ALR88588 342 –153
ENSG00000148288 Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 91 Bacteria A8QE87 39 Cimex lectularis XP_014240367.1 37 93
ENSG00000154122 Ankylosis, progressive homolog (mouse) 129 Protist F5GXN7 90 S. kowalevskii XP_006818212 388 –169
ENSG00000172757 Cofilin 1 31 Fungi B3S0K8 80 Helobdella robusta XP_009011217 108 3
ENSG00000175573 Chromosome 11 open reading frame 68 60 Fungi D6WQ69 48 S. kowalevskii XP_002740403.1 157 –49
ENSG00000177181 Ribosomal modification protein rimK-like family member A 74 Archaea E1GHX3 52 Aplysia californica XP_012936156 124 2
ENSG00000212907 Mitochondrially encoded NADH dehydrogenase 4 L 69 Protist P15554 68 Xenoturbella bocki YP_850984 67 71
ENSG00000216937 Coiled-coil domain containing protein 7 48 Protist A7SDV0 64 No hits    
ENSG00000242265 Retrotransposon-derived protein PEG10 52 Fungi G0MWG3 49 No hits    
ENSG00000256062 ABO blood group (Histo-blood group ABO system transferase) 84 Bacteria H3INK7 37 S. kowalevskii XM_006825840 218 –97
  1. The HGT index, defined by Crisp et al. [1] as the difference in the best bitscore of a BLAST match to a non-metazoan and a metazoan species, is shown along with the bitscore of the best metazoan match. The best metazoan match excluded any matches to the phylum Chordata for these human genes. All of the genes in this table were reported by Crisp et al. [1] as high-confidence (class A) HGT. The recomputed HGT index (last column) is computed by subtracting the bitscore of best non-metazoan found by Crisp et al. [1] from that of the best non-chordate metazoans found by the new searches reported here. “No hits” means that no significant alignments were found to any non-chordate metazoans
  2. aFor PRAME family members 1, 6, and 15, the protist alignment found by Crisp et al. [1] is a false positive caused by contamination. See main text for details