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Table 1 List of candidate genes after extracting non-synonymous colour genes and testing with Sanger sequencing

From: A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama)

Chr

Chr_pos

Ref

Alt

Gene

Acc.No.

SNP

Codon

aa subst.

13

51,640,322

C

T

ATRN

NM_173995.3

c.1573C > T

Gat/Aat

p.D525NN

23

41,483,931

G

C

DTNBP1

NM_001045947.1

c.871G > C

Gcc/Ccc

p.A291P

26

22,870,530

A

G

ELOVL3

NM_001192306.1

c.73A > G

Aac/Gac

p.N25D

12

23,298,094

C

T

FREM2

XM_002691799.5

c.9260C > T

aGg/aAg

p.R3087K

12

23,336,198

G

T

FREM2

XM_002691799.5

c.6042G > T

gaC/gaA

p.D2014E

17

71,465,091

T

C

GGT1

NM_001206214.1

c.100 T > C

Agc/Ggc

p.S34G

28

4,036,781

G

A

GNPAT

NM_001103286.1

c.1462G > A

Gtt/Att

p.V488I

X

37,080,066

C

T

L1CAM

NM_001192435.1

c.2722C > T

Ggg/Agg

p.G908R

28

8,475,854

A

C

LYST

NM_174020.2

c.5337A > C

ttA/ttC

p.L1779F

18

14,705,518

T

C

MC1R

NM_174108.2

c.143 T > C

cTg/cCg

p.L48P

11

103,981,017

T

G

NOTCH1

XM_024999642.1

c.43 T > G

Aca/Cca

p.T15P

3

13,984,639

T

C

NTRK1

XM_024989930.1

c.55 T > C

Agg/Ggg

p.R19G

5

57,353,185

T

C

PMEL

NM_001080215.2

c.1873 T > C

Tgg/Cgg

p.W625R

14

429,568

A

G

RECQL4

NM_001098037.2

c.370A > G

Acc/Gcc

p.T124A

14

429,631

T

C

RECQL4

NM_001098037.2

c.433 T > C

Tca/Cca

p.S145P

4

40,075,565

G

A

SEMA3C

NM_001101082.1

c.718G > A

Gtg/Atg

p.V240M

3

14,622,613

C

G

SEMA4A

NM_001075440.1

c.320C > G

aGt/aCt

p.S107T

X

133,162,026

G

T

SHROOM2

XM_002700461.5

c.3176G > T

gCc/gAc

p.A1059D

X

133,162,029

G

A

SHROOM2

XM_002700461.5

c.3173G > A

tCc/tTc

p.S1058F

  1. Chr Bos taurus reference chromosome; Chr_pos position on the bovine chromosome (in bp); Ref reference nucleotide; Alt alternative nucleotide; Gene gene name; Acc.No. accession number of the NCBI reference sequence; SNP polymorphism in the NCBI reference sequence; Codon codon with SNP in capital letters; aa subst. amino acid substitution (according to the protein_id given in the NCBI reference sequence)