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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