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. 2018 Jun 4;70(9):571–583. doi: 10.1007/s00251-018-1064-4

Nomenclature for the KIR of non-human species

James Robinson 1,2, Lisbeth A Guethlein 3, Giuseppe Maccari 1,4, Jeroen Blokhuis 5,6, Benjamin N Bimber 7, Natasja G de Groot 5, Nicholas D Sanderson 4,8, Laurent Abi-Rached 9, Lutz Walter 10, Ronald E Bontrop 5, John A Hammond 4, Steven G E Marsh 1,2,✉, Peter Parham 3
PMCID: PMC6096839  PMID: 29869002

Abstract

The increasing number of Killer Immunoglobulin-like Receptor (KIR) sequences available for non-human primate species and cattle has prompted development of a centralized database, guidelines for a standardized nomenclature, and minimum requirements for database submission. The guidelines and nomenclature are based on those used for human KIR and incorporate modifications made for inclusion of non-human species in the companion IPD-NHKIR database. Included in this first release are the rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), orangutan (Pongo abelii and Pongo pygmaeus), and cattle (Bos taurus).

Keywords: KIR, Nomenclature, Variant, Allele, Gene, Database, Sequence

Introduction

The KIR locus has been studied in a number of non-human species primates and is characterized by high levels of allelic polymorphism, haplotypic polymorphism in the number of genes, and extensive duplication and recombination (Hammond et al. 2016; Parham 2004). These factors have made it difficult to assign orthologues and have led to a number of different nomenclature systems being used to name genes and alleles. This report describes a common framework and guidelines for KIR nomenclature in non-human species. These have been developed by taking advantage of lessons learned in the development of a nomenclature system for the human KIR (Marsh et al. 2003).

General naming guidelines

To provide consistency with the IPD-MHC Database (Maccari et al. 2017), the non-human KIR nomenclature adopts the same four-character prefix used for species designation in the naming of MHC alleles (de Groot et al. 2012; Ellis et al. 2006; Klein et al. 1990). Also, genes and alleles will be named based on the conventions that have been adopted for the human KIR system (Marsh et al. 2003) that are based on the structures of the molecules they encode. The first digit following the KIR acronym corresponds to the number of Ig-like domains in the polypeptide and the “D” denotes “Domain.” The D is followed by either an “L” indicating a “Long” cytoplasmic tail, an “S” indicating a “Short” cytoplasmic tail or a “P” for pseudogenes. In addition, the inclusion of a “W” indicates “Workshop” following the “L,” “S,” or “P” to indicate any sequence that by phylogenetic analysis is sufficiently divergent to be considered a “new” gene, but lack either genomic sequencing or family studies to demonstrate that it does define a new gene and not a divergent lineage a known gene. Tables 1, 2, and 3 list the current gene designations and their previous names. Symbols for genes are italicized (e.g., Mamu-KIR3DL01), whereas symbols for proteins are not italicized (e.g., Mamu-KIR3DL01). Alleles follow the same conventions as gene names.

Table 1.

Gene designations and their previous names

Species KIR gene designation(s) Previous KIR gene designation(s)
Rhesus macaque (Mamu) Mamu-KIR1D KIR1D, Mamu-KIR1D
Mamu-KIR2DL04 2DL501NK, 2DL503NK, KIR2DL4, KIR2DL4.1, MmKIR2DL4
Mamu-KIR3DL01 2DL426NK, 3DL34, KIR3DL, KIR3DL-like_1, KIR3DL1, KIR3DL1-like1, KIR3DL12, KIR3DL13, KIR3DL14, KIR3DL15, KIR3DL19, KIR3DL1_variant_2, KIR3DL2, KIR3DL2-old, KIR3DL3, KIR3DL4, KIR3DL5
Mamu-KIR3DL02 KIR3DL-like_3, KIR3DL2, KIR3DL21, KIR3DL21-like1
Mamu-KIR3DL04 KIR3DL11
Mamu-KIR3DL05 3DL7b-3DL40, KIR3DL, KIR3DL-3, KIR3DL16, KIR3DL7, KIR3DL7-like2, KIR3DL07
Mamu-KIR3DL06 KIR3DL6
Mamu-KIR3DL07 2DL420, KIR3DL, KIR3DL18, KIR3DL7, KIR3DL7-like1, KIR3DL7-like3, KIR3DL03
Mamu-KIR3DL08 KIR3DL, KIR3DL-like_2, KIR3DL17, KIR3DL8, KIRDL8, Mamu-KIR3DL04, Mamu-KIR3DL4
Mamu-KIR3DL10 3DL10-2DL501, 3DL3NK, KIR3DL, KIR3DL10, KIR3DL9, Mamu-KIR3DL05
Mamu-KIR3DL11 KIR3DL, KIR3DL-1, KIR3DL-6, KIR3DL-7, KIR3DL11
Mamu-KIR3DL20 KIR3DL20, KIR3DL20_variant_2, KIR3DL06, KIR2DL5
Mamu-KIR3DLW03 KIR3DL-4, KIR3DL-5, KIR3DL-like1-BNB, KIR3DL21
Mamu-KIR3DLX1 KIR3DL0
Mamu-KIR3DS01 KIR3DH-7, KIR3DH1, KIR3DH5, Mamu-KIR3DS01-JHB-HEFGH,
Mamu-KIR3DS02 3DH2, 3DH42, KIR3DH-like_5, KIR3DH-like_6, KIR3DH10, KIR3DH12, KIR3DH13, KIR3DH14, KIR3DH15, KIR3DH16, KIR3DH2
Mamu-KIR3DS03 KIR3DH3, KIR3DH8, KIR3DH9
Mamu-KIR3DS04 KIR3DH-1, KIR3DH4, KIR3DH6
Mamu-KIR3DS05 KIR3DH1, KIR3DM-1, KIR3DM1, KIR3DM6, KIR_Partial_Sequence_1
Mamu-KIR3DS06 KIR3DH-4, KIR3DH-like8, KIR3DH-like_7, KIR3DH18,
Mamu-KIR3DSW07 KIR3DH-5, KIR3DH7, Mamu-KIR3DS07-JHB-HO
Mamu-KIR3DSW08 KIR3DH-2, KIR3DH-3, KIR3DH-4, KIR3DH-5, KIR3DH-like_1, KIR3DH-like_2, KIR3DH-like_3, KIR3DH-like_4, KIR3DH21, KIR3DSW08
Mamu-KIR3DSW09 KIR3DH-8, KIR3DH20, KIR3DH5, KIR3DH5-like1, mmKIR3DH-1
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Table 2.

Gene designations and their previous names

Species KIR gene designation(s) Previous KIR gene designation(s)
Chimpanzee (Patr) Patr-KIR2DL4
Patr-KIR2DL5
Patr-KIR2DL6 Pt-NewII
Patr-KIR2DL7
Patr-KIR2DL8 Pt-NewIII
Patr-KIR2DL9
Patr-KIR3DL1 Pt-KIR3DL1/2, Pt-KIR3DL3, Pt-KIR3DL1, Pt-KIR3DL2
Patr-KIR3DL3 Patr-KIRC1, Pt-NewI
Patr-KIR3DL4
Patr-KIR3DL5
Patr-KIR3DS6 Pt-KIR3DL6
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Table 3.

Gene designations and their previous names

Species KIR gene designation(s) Previous KIR gene designation(s)
Orangutan (Poab) Poab-KIR2DL10 Popy-KIR2DL10, 2DLA
Poab-KIR2DL11 Popy-KIR2DL11, 2DLB
Poab-KIR2DL12 Popy-KIR2DL11, 2DLC
Poab-KIR2DL5 Popy-KIR2DL5. 2DL5
Poab-KIR2DS10 2DSD/2DSA
Poab-KIR2DS13 Popy-KIR2DS13, 2DSC1/2DSB
Poab-KIR2DS14 Popy-KIR2DS14, 2DSB/2DSD2, 2DSA/2DSD1
Poab-KIR3DL1 Popy-KIR3DL1, 3DLH, 3DLC, 3DLD2, 3DLD1, 3DLA, 3DLI, 3DLB
Poab-KIR3DL3 Popy-KIR3DL3, 3DL3
Poab-KIR3DS1 Popy-KIR3DS1, 3DS1
Poab-KIRDP Popy-KIRDP, DP
Orangutan (Popy) Popy-KIR2DL11 Popy-KIR2DLB
Popy-KIR2DL12 Popy-KIR2DLC
Popy-KIR2DL5
Popy-KIR2DS10 Popy-KIR2DSD/2DSA
Popy-KIR2DS13 Popy-KIR2DSC2/2DSB
Popy-KIR2DS14 Popy-KIR2DSB/2DSD2, 2DSA/2DSD1
Popy-KIR2DS15
Popy-KIR3DL1 Popy-KIR3DL1, 3DLF, 3DLE2, 3DLE1
Popy-KIR3DL3 Popy-KIR3DL3, 3DL3
Popy-KIR3DS1 Popy-KIR3DS1, 3DS1
Popy-KIRDP Popy-KIRDP, DP
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Reflecting species-specific differences, there have been further additions/modifications to the general nomenclature for rhesus macaque and cattle. As with the human KIR nomenclature, alleles in each series have been named in order of their deposition into a generalist sequence databank, GenBank/EMBL-ENA/DDBJ (Benson et al. 2017; Chojnacki et al. 2017; Mashima et al. 2017). Where the identity is known of the animal providing the sequenced DNA, that information is included in the database, as well as information regarding the origin of the animal. Tables 4, 5, 6, and 7 provide a complete list of genes and alleles currently in the nomenclature, as well as the original name(s), accession number, and reference to the original report of the sequence.

Table 4.

Allele designations and their previous names

Gene Allele designation Previous designations Accession number Reference
Mamu-KIR1D Mamu-KIR1D*001 KIR1D AF334634 (Hershberger et al. 2001)
Mamu-KIR1D Mamu-KIR1D*002 KIR1D,Mamu-KIR1D*00202-JHB-HA AY728181, GU112257, GU112266, GU112332 (Sambrook et al. 2005) (Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*001:01 KIR2DL4, KIR2DL4.1, MmKIR2DL4*0010101-JHB EU702486, AF361088, AF334644, FJ824091, GU112331, GU112318, GU112263, GU112303, GU112287 (Blokhuis et al. 2009a; Blokhuis et al. 2009b; Blokhuis et al. 2010; Grendell et al. 2001; Hershberger et al. 2001)
Mamu-KIR2DL04 Mamu-KIR2DL04*001:02 2DL501NK GU299490 (Colantonio et al. 2011)
Mamu-KIR2DL04 Mamu-KIR2DL04*002 MmKIR2DL4*0020101-JHB FJ824092, GU112279 (Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*003 KIR2DL4, MmKIR2DL4*0040101-JHB AY505486, FJ824093, GU112322, GU112284 (Andersen et al. 2004; Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*004 KIR2DL4 AY728182 (Sambrook et al. 2005)
Mamu-KIR2DL04 Mamu-KIR2DL04*005 MmKIR2DL4*0050101-JHB FJ824094 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*006:01 MmKIR2DL4*0060101-JHB FJ824095 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*006:02 2DL503NK GU014298 (Colantonio et al. 2011)
Mamu-KIR2DL04 Mamu-KIR2DL04*007 MmKIR2DL4*0070101-JHB FJ824096 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*008:01 MmKIR2DL4*0080101-JHB FJ824097 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*008:02 MmKIR2DL4*0080201-JHB FJ824098, GU112326 (Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*010 MmKIR2DL4*0100101-JHB FJ824100 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*011 MmKIR2DL4*0110101-JHB FJ824101 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*012 MmKIR2DL4*0120101-JHB FJ824102 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*013 MmKIR2DL4*0130101-JHB FJ824103 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*014:01 MmKIR2DL4*0140101-JHB FJ824104, GU112316 (Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*014:02 MmKIR2DL4*0140201-JHB FJ824105 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*015:01 MmKIR2DL4*0150101-JHB FJ824106, GU112313 (Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*015:02 MmKIR2DL4*0150201-JHB FJ824107, GU112280 (Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR2DL04 Mamu-KIR2DL04*016 MmKIR2DL4*0160101-JHB FJ824108 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*017 MmKIR2DL4*0170101-JHB FJ824109 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*018 MmKIR2DL4*0180101-JHB FJ824110 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*019 MmKIR2DL4*0190101-JHB FJ824111 (Blokhuis et al. 2009b)
Mamu-KIR2DL04 Mamu-KIR2DL04*020 MmKIR2DL4*0200101-JHB FJ824112, GU112274 (Blokhuis et al. 2009b; Blokhuis et al. 2010)
Mamu-KIR3DL01 Mamu-KIR3DL01*001 KIR3DL1, 3DL34 AF334616, GU299488 (Colantonio et al. 2011; Hershberger et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*002 KIR3DL2-old, 2DL426NK AF334617, GU299488 (Hershberger et al. 2001), (Colantonio et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*003 KIR3DL3 AF361083, GU112305 (Blokhuis et al. 2010; Grendell et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*004 KIR3DL4 AF334619 (Hershberger et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*005 KIR3DL5 AF334620 (Hershberger et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*006 KIR3DL12 AF361082 (Grendell et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*007N KIR3DL13 AF408151 (Grendell et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*008N KIR3DL14 AF408152 (Grendell et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*009N KIR3DL15 AF408153 (Grendell et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*010 KIR3DL19 AF408150 (Grendell et al. 2001)
Mamu-KIR3DL01 Mamu-KIR3DL01*011 KIR3DL1_variant_2 AY728187 (Sambrook et al. 2005)
Mamu-KIR3DL01 Mamu-KIR3DL01*012 KIR3DL1*002-BNB, KIR3DL-like_1 EU419033, AY505476, GU112286 (Andersen et al. 2004; Blokhuis et al. 2010; Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*013 KIR3DL1*003-BNB EU419034 (Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*014 KIR3DL1*005-BNB EU419035 (Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*015 KIR3DL1*006-BNB EU419036 (Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*016 KIR3DL1*007-BNB EU419037, GU112258 (Blokhuis et al. 2010; Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*017 KIR3DL12*001-BNB EU419044 (Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*018 KIR3DL2*001-BNB EU419046 (Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*019:01 KIR3DL1*001-BNB EU419032, GU112300 (Blokhuis et al. 2010; Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*019:02 None GU112283 (Blokhuis et al. 2010)
Mamu-KIR3DL01 Mamu-KIR3DL01*020 KIR3DL1-like1 EU688987 (Moreland et al. 2011)
Mamu-KIR3DL01 Mamu-KIR3DL01*021 KIR3DL FJ562108 (Bostik et al. 2009)
Mamu-KIR3DL01 Mamu-KIR3DL01*022 None GU112267 (Blokhuis et al. 2010)
Mamu-KIR3DL01 Mamu-KIR3DL01*023 None GU112292 (Blokhuis et al. 2010)
Mamu-KIR3DL01 Mamu-KIR3DL01*024 None GU112321 (Blokhuis et al. 2010)
Mamu-KIR3DL01 Mamu-KIR3DL01*025 None GU112324 (Blokhuis et al. 2010)
Mamu-KIR3DL01 Mamu-KIR3DL01*026 KIR3DL allele 2 FJ562109 (Bostik et al. 2009)
Mamu-KIR3DL01 Mamu-KIR3DL01*027 KIR3DL allele 3 FJ562110 (Bostik et al. 2009)
Mamu-KIR3DL02 Mamu-KIR3DL02*001 KIR3DL2 AY728188 (Sambrook et al. 2005)
Mamu-KIR3DL02 Mamu-KIR3DL02*002 KIR3DL-like_3 AY505478 (Andersen et al. 2004)
Mamu-KIR3DL02 Mamu-KIR3DL02*003 KIR3DL21*001-BNB EU419050 (Moreland et al. 2011)
Mamu-KIR3DL02 Mamu-KIR3DL02*004:01 KIR3DL21*003-BNB EU419052 (Moreland et al. 2011)
Mamu-KIR3DL02 Mamu-KIR3DL02*004:02 KIR3DL21*005-BNB EU419053 (Moreland et al. 2011)
Mamu-KIR3DL02 Mamu-KIR3DL02*005 KIR3DL21*006-BNB EU419054 (Moreland et al. 2011)
Mamu-KIR3DL02 Mamu-KIR3DL02*006 KIR3DL21-like1 EU688989 (Moreland et al. 2011)
Mamu-KIR3DL02 Mamu-KIR3DL02*007 None GU112277 (Blokhuis et al. 2010)
Mamu-KIR3DL02 Mamu-KIR3DL02*008 None GU112281 (Blokhuis et al. 2010)
Mamu-KIR3DLW03 Mamu-KIR3DLW03*001 KIR3DL21*002-BNB EU419051 (Moreland et al. 2011)
Mamu-KIR3DLW03 Mamu-KIR3DLW03*002 KIR3DL21*007-BNB EU419055 (Moreland et al. 2011)
Mamu-KIR3DLW03 Mamu-KIR3DLW03*003 KIR3DL-like1-BNB EU419031 (Moreland et al. 2011)
Mamu-KIR3DLW03 Mamu-KIR3DLW03*004 KIR3DL-4 FN424253 (Kruse et al. 2010)
Mamu-KIR3DLW03 Mamu-KIR3DLW03*005 KIR3DL-5 FN424256 (Kruse et al. 2010)
Mamu-KIR3DL04 Mamu-KIR3DL04*001:01 KIR3DL11*002-BNB EU419040 (Moreland et al. 2011)
Mamu-KIR3DL04 Mamu-KIR3DL04*001:02 None GU112311 (Blokhuis et al. 2010)
Mamu-KIR3DL04 Mamu-KIR3DL04*001:03 None GU112319 (Blokhuis et al. 2010)
Mamu-KIR3DL04 Mamu-KIR3DL04*002 KIR3DL11*003-BNB EU419042 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*001 KIR3DL16*001-BNB EU419045 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*002 KIR3DL7*004-BNB EU419061 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*003 KIR3DL7*005-BNB EU419062 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*004 KIR3DL7*009-BNB EU419066 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*005 KIR3DL7*013-BNB EU419069 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*006:01 KIR3DL7-like2 EU688991 (Moreland et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*006:02 None GU112293 (Blokhuis et al. 2010)
Mamu-KIR3DL05 Mamu-KIR3DL05*007 KIR3DL-3 FN424252 (Kruse et al. 2010)
Mamu-KIR3DL05 Mamu-KIR3DL05*008 3DL7b-3DL40 GU112291, GU014295 (Blokhuis et al. 2010) (Colantonio et al. 2011)
Mamu-KIR3DL05 Mamu-KIR3DL05*009 None GU112310 (Blokhuis et al. 2010)
Mamu-KIR3DL05 Mamu-KIR3DL05*010 KIR3DL allele 13 FJ562120 (Bostik et al. 2009)
Mamu-KIR3DL05 Mamu-KIR3DL05*011 KIR3DL allele 14 FJ562121 (Bostik et al. 2009)
Mamu-KIR3DL06 Mamu-KIR3DL06*001 KIR3DL6 AF334621 (Hershberger et al. 2001)
Mamu-KIR3DL06 Mamu-KIR3DL06*002 KIR3DL6*001-BNB EU419056 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*001 KIR3DL7 AF334622 (Hershberger et al. 2001)
Mamu-KIR3DL07 Mamu-KIR3DL07*002 KIR3DL18 AF361086 (Grendell et al. 2001)
Mamu-KIR3DL07 Mamu-KIR3DL07*003 KIR3DL7*001-BNB EU419057 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*004 KIR3DL7*003-BNB EU419060 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*005 KIR3DL7*006-BNB EU419063 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*006 KIR3DL7*007-BNB EU419064 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*007 KIR3DL7*008-BNB EU419065 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*008 KIR3DL7*012-BNB EU419068 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*009:01 KIR3DL7-like1, 2DL420 EU688990, GU299489 (Colantonio et al. 2011; Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*009:02 None GU112282 (Blokhuis et al. 2010)
Mamu-KIR3DL07 Mamu-KIR3DL07*010 KIR3DL7-like3 EU688992 (Moreland et al. 2011)
Mamu-KIR3DL07 Mamu-KIR3DL07*011 KIR3DL allele 10 FJ562117 (Bostik et al. 2009)
Mamu-KIR3DL07 Mamu-KIR3DL07*012 KIR3DL allele 11 FJ562118 (Bostik et al. 2009)
Mamu-KIR3DL08 Mamu-KIR3DL08*001:01 KIR3DL8 AY728189 (Sambrook et al. 2005)
Mamu-KIR3DL08 Mamu-KIR3DL08*001:02 KIR3DL8*002-BNB EU419071 (Moreland et al. 2011)
Mamu-KIR3DL08 Mamu-KIR3DL08*002 KIR3DL17 AF361084, GU112306 (Blokhuis et al. 2010; Grendell et al. 2001)
Mamu-KIR3DL08 Mamu-KIR3DL08*003 KIR3DL17 AF361085 (Grendell et al. 2001)
Mamu-KIR3DL08 Mamu-KIR3DL08*004 KIR3DL-like_2 AY505477 (Andersen et al. 2004)
Mamu-KIR3DL08 Mamu-KIR3DL08*005 KIRDL8 AY728189 (Sambrook et al. 2005)
Mamu-KIR3DL08 Mamu-KIR3DL08*006 KIR3DL8*001-BNB EU419070 (Moreland et al. 2011)
Mamu-KIR3DL08 Mamu-KIR3DL08*007 None GU112268 (Blokhuis et al. 2010)
Mamu-KIR3DL08 Mamu-KIR3DL08*008 None GU112285 (Blokhuis et al. 2010)
Mamu-KIR3DL08 Mamu-KIR3DL08*009 None GU112290 (Blokhuis et al. 2010)
Mamu-KIR3DL08 Mamu-KIR3DL08*010 None GU112330 (Blokhuis et al. 2010)
Mamu-KIR3DL08 Mamu-KIR3DL08*011 KIR3DL allele 8 FJ562115 (Bostik et al. 2009)
Mamu-KIR3DL10 Mamu-KIR3DL10*001 KIR3DL10 AY728183 (Sambrook et al. 2005)
Mamu-KIR3DL10 Mamu-KIR3DL10*002:01 KIR3DL9, KIR3DL allele 5 AF334624, GU112259, FJ562112 (Hershberger et al. 2001)(Blokhuis et al. 2010; Bostik et al. 2009)
Mamu-KIR3DL10 Mamu-KIR3DL10*002:02 3DL3NK GU299486 (Colantonio et al. 2011)
Mamu-KIR3DL10 Mamu-KIR3DL10*003 KIR3DL10*001-BNB EU419038 (Moreland et al. 2011)
Mamu-KIR3DL10 Mamu-KIR3DL10*004 KIR3DL10*002-BNB EU419039 (Moreland et al. 2011)
Mamu-KIR3DL10 Mamu-KIR3DL10*005:01 3DL10-2DL501 GU014294 (Colantonio et al. 2011)
Mamu-KIR3DL10 Mamu-KIR3DL10*005:02 None GU112295 (Blokhuis et al. 2010)
Mamu-KIR3DL10 Mamu-KIR3DL10*006 KIR3DL allele 6 FJ562113 (Bostik et al. 2009)
Mamu-KIR3DL11 Mamu-KIR3DL11*001 KIR3DL11 AF334626, GU112271 (Blokhuis et al. 2010; Hershberger et al. 2001)
Mamu-KIR3DL11 Mamu-KIR3DL11*002 KIR3DL-1 FN424250 (Kruse et al. 2010)
Mamu-KIR3DL11 Mamu-KIR3DL11*003 KIR3DL-6 FN424259 (Kruse et al. 2010)
Mamu-KIR3DL11 Mamu-KIR3DL11*004 KIR3DL-7 FN424261 (Kruse et al. 2010)
Mamu-KIR3DL11 Mamu-KIR3DL11*005 None GU112276 (Blokhuis et al. 2010)
Mamu-KIR3DL11 Mamu-KIR3DL11*006 None GU112296 (Blokhuis et al. 2010)
Mamu-KIR3DL11 Mamu-KIR3DL11*007 KIR3DL allele 9 FJ562116 (Bostik et al. 2009)
Mamu-KIR3DL20 Mamu-KIR3DL20*001 KIR3DL20*001-BNB EU419047 (Moreland et al. 2011)
Mamu-KIR3DL20 Mamu-KIR3DL20*002 KIR3DL20 AY728184, GU112327 (Blokhuis et al. 2010; Sambrook et al. 2005)
Mamu-KIR3DL20 Mamu-KIR3DL20*003 KIR3DL20_variant_2 AY728186 (Sambrook et al. 2005)
Mamu-KIR3DL20 Mamu-KIR3DL20*004 KIR3DL20*003-BNB EU419048 (Moreland et al. 2011)
Mamu-KIR3DL20 Mamu-KIR3DL20*005 KIR3DL20*004-BNB EU419049 (Moreland et al. 2011)
Mamu-KIR3DL20 Mamu-KIR3DL20*006 None GU112255 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*007 None GU112256 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*008 None GU112264 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*009 None GU112270 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*010 None GU112275 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*011 None GU112289 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*012 None GU112299 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*013 None GU112304, GU112317 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*014 None GU112308 (Blokhuis et al. 2010)
Mamu-KIR3DL20 Mamu-KIR3DL20*015 None GU134802 (Blokhuis et al. 2010)
Mamu-KIR3DS01 Mamu-KIR3DS01*001:01 KIR3DH5 AF361087 (Grendell et al. 2001)
Mamu-KIR3DS01 Mamu-KIR3DS01*001:02 None GU112307 (Blokhuis et al. 2010)
Mamu-KIR3DS01 Mamu-KIR3DS01*002 KIR3DH1 AY728190 (Sambrook et al. 2005)
Mamu-KIR3DS01 Mamu-KIR3DS01*003 KIR3DH-7 GU564161 (Chaichompoo et al. 2010)
Mamu-KIR3DS02 Mamu-KIR3DS02*001 KIR3DH2 AF334649 (Hershberger et al. 2001)
Mamu-KIR3DS02 Mamu-KIR3DS02*002 KIR3DH-like_5 AY505483 (Andersen et al. 2004)
Mamu-KIR3DS02 Mamu-KIR3DS02*003 KIR3DH-like_6 AY505484 (Andersen et al. 2004)
Mamu-KIR3DS02 Mamu-KIR3DS02*004:01 KIR3DH2*001-BNB, KIR3DH14 EU419026, EU702460 (Blokhuis et al. 2009a; Moreland et al. 2011)
Mamu-KIR3DS02 Mamu-KIR3DS02*004:02 KIR3DH13, 3DH42 EU702459, GU014296 (Blokhuis et al. 2009a) (Colantonio et al. 2011)
Mamu-KIR3DS02 Mamu-KIR3DS02*004:03 KIR3DH12 EU702458 (Blokhuis et al. 2009a)
Mamu-KIR3DS02 Mamu-KIR3DS02*005 KIR3DH2*002-BNB EU419027 (Moreland et al. 2011)
Mamu-KIR3DS02 Mamu-KIR3DS02*006 KIR3DH16 EU702462 (Blokhuis et al. 2009a)
Mamu-KIR3DS02 Mamu-KIR3DS02*007 KIR3DH15 EU702461 (Blokhuis et al. 2009a)
Mamu-KIR3DS02 Mamu-KIR3DS02*008 KIR3DH10 EU702456, GU112278 (Blokhuis et al. 2009a; Blokhuis et al. 2010)
Mamu-KIR3DS02 Mamu-KIR3DS02*009 None GU112261, GU112315 (Blokhuis et al. 2010)
Mamu-KIR3DS02 Mamu-KIR3DS02*010 None GU112297 (Blokhuis et al. 2010)
Mamu-KIR3DS02 Mamu-KIR3DS02*011 None GU112323 (Blokhuis et al. 2010)
Mamu-KIR3DS02 Mamu-KIR3DS02*012 3DH2*NEW1 JN613291 (Hellmann et al. 2011)
Mamu-KIR3DS02 Mamu-KIR3DS02*013 3DH2*NEW1 JN613299 (Hellmann et al. 2011)
Mamu-KIR3DS03 Mamu-KIR3DS03*001:01 KIR3DH3 AF334650, GU112312 (Hershberger et al. 2001) (Blokhuis et al. 2010)
Mamu-KIR3DS03 Mamu-KIR3DS03*001:02 None GU112294 (Blokhuis et al. 2010)
Mamu-KIR3DS03 Mamu-KIR3DS03*002 KIR3DH9 EU702455, GU112269 (Blokhuis et al. 2009a; Blokhuis et al. 2010)
Mamu-KIR3DS03 Mamu-KIR3DS03*003 KIR3DH8 EU702454 (Blokhuis et al. 2009a)
Mamu-KIR3DS04 Mamu-KIR3DS04*001 KIR3DH4 AF334651 (Hershberger et al. 2001)
Mamu-KIR3DS04 Mamu-KIR3DS04*002 KIR3DH4*001-BNB EU419028 (Moreland et al. 2011)
Mamu-KIR3DS04 Mamu-KIR3DS04*003 KIR3DH4*002-BNB, KIR3DH4 EU419029, JN613296 (Hellmann et al. 2011; Moreland et al. 2011)
Mamu-KIR3DS04 Mamu-KIR3DS04*004 KIR3DH6 EU702452 (Blokhuis et al. 2009a)
Mamu-KIR3DS04 Mamu-KIR3DS04*005 KIR3DH4 JN613300 (Hellmann et al. 2011)
Mamu-KIR3DS04 Mamu-KIR3DS04*006 KIR3DH-1 GU564157 (Chaichompoo et al. 2010)
Mamu-KIR3DS05 Mamu-KIR3DS05*001 KIR3DH1*001-BNB EU419024, EU419025, EU702468, AY505487, GU112262 (Moreland et al. 2011)
Mamu-KIR3DS05 Mamu-KIR3DS05*002:01 KIR3DH1*002-BNB, KIR3DM1, KIR_Partial_Sequence_1 EU419025, EU702468, AY505487, GU112262 (Andersen et al. 2004; Blokhuis et al. 2009a; Blokhuis et al. 2010; Moreland et al. 2011)
Mamu-KIR3DS05 Mamu-KIR3DS05*002:02 KIR3DM6 EU702473 (Blokhuis et al. 2009a)
Mamu-KIR3DS05 Mamu-KIR3DS05*003 KIR3DM-1 FN424260 (Kruse et al. 2010)
Mamu-KIR3DS06 Mamu-KIR3DS06*001 KIR3DH-like_7 AY505485 (Andersen et al. 2004)
Mamu-KIR3DS06 Mamu-KIR3DS06*002:01 KIR3DH-like8 EU688985 (Moreland et al. 2011)
Mamu-KIR3DS06 Mamu-KIR3DS06*002:02 None GU112298 (Blokhuis et al. 2010)
Mamu-KIR3DS06 Mamu-KIR3DS06*003 KIR3DH18 EU702464 (Blokhuis et al. 2009a)
Mamu-KIR3DS06 Mamu-KIR3DS06*004 KIR3DH-4 FN424257 (Kruse et al. 2010)
Mamu-KIR3DS06 Mamu-KIR3DS06*005 None GU112260 (Blokhuis et al. 2010)
Mamu-KIR3DS06 Mamu-KIR3DS06*006 None GU112314 (Blokhuis et al. 2010)
Mamu-KIR3DSW07 Mamu-KIR3DSW07*001 KIR3DH7 EU702453, GU112272 (Blokhuis et al. 2009a; Blokhuis et al. 2010)
Mamu-KIR3DSW07 Mamu-KIR3DSW07*002 KIR3DH-5 FN424258 (Kruse et al. 2010)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*001 KIR3DH-like_1 AY505479 (Andersen et al. 2004)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*002 KIR3DH-like_2 AY505480 (Andersen et al. 2004)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*003 KIR3DH-like_3 AY505481 (Andersen et al. 2004)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*004 KIR3DH-like_4 AY505482 (Andersen et al. 2004)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*005 KIR3DH21 EU702467 (Blokhuis et al. 2009a)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*006 KIR3DH-2 FN424254 (Kruse et al. 2010)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*007 KIR3DH-3 FN424255 (Kruse et al. 2010)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*008 None GU112325 (Blokhuis et al. 2010)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*009 None GU112328 (Blokhuis et al. 2010)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*010 KIR3DSW08 JN613297 (Hellmann et al. 2011)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*011 KIR3DH-4 GU564158 (Chaichompoo et al. 2010)
Mamu-KIR3DSW08 Mamu-KIR3DSW08*012 KIR3DH-5 GU564159 (Chaichompoo et al. 2010)
Mamu-KIR3DSW09 Mamu-KIR3DSW09*001 KIR3DH5*001-BNB EU419030 (Moreland et al. 2011)
Mamu-KIR3DSW09 Mamu-KIR3DSW09*002 KIR3DH5-like1 EU688986 (Moreland et al. 2011)
Mamu-KIR3DSW09 Mamu-KIR3DSW09*003 None GU112301 (Blokhuis et al. 2010)
Mamu-KIR3DSW09 Mamu-KIR3DSW09*004 KIR3DH20 EU702466, GU112273 (Blokhuis et al. 2009a), (Blokhuis et al. 2010)
Mamu-KIR3DSW09 Mamu-KIR3DSW09*005 mmKIR3DH-1 FN424249 (Kruse et al. 2010)
Mamu-KIR3DSW09 Mamu-KIR3DSW09*006 KIR3DH-8 GU564162 (Chaichompoo et al. 2010)
Mamu-KIR3DLX1 Mamu-KIR3DLX1*001 KIR3DL0 DQ157756 (Sambrook et al. 2006)
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Table 5.

Allele designations and their previous names

Gene Allele designation Previous designations Accession number Reference
Patr-KIR2DL4 Patr-KIR2DL4*001 None HM068617 (Abi-Rached et al. 2010)
Patr-KIR2DL4 Patr-KIR2DL4*002 None AC155174, AF258804 (Khakoo et al. 2000)
Patr-KIR2DL4 Patr-KIR2DL4*003 None BX842589 (Sambrook et al. 2005)
Patr-KIR2DL5 Patr-KIR2DL5*001 None HM068617 (Abi-Rached et al. 2010)
Patr-KIR2DL5 Patr-KIR2DL5*002 None AF274005 (Rajalingam et al. 2001)
Patr-KIR2DL5 Patr-KIR2DL5*003 None AC155174
Patr-KIR2DL5 Patr-KIR2DL5*004 None BX842589 (Sambrook et al. 2005)
Patr-KIR2DL5 Patr-KIR2DL5*005 None AF258805 (Khakoo et al. 2000)
Patr-KIR2DL6 Patr-KIR2DL6*001 None BX842589, AM292662 (Sambrook et al. 2005)
Patr-KIR2DL6 Patr-KIR2DL6*002 None AF258806
Patr-KIR2DL6 Patr-KIR2DL6*003 None AM292661
Patr-KIR2DL7 Patr-KIR2DL7*001 None HM068617 (Abi-Rached et al. 2010)
Patr-KIR2DL8 Patr-KIR2DL8*001 None HM068617 (Abi-Rached et al. 2010)
Patr-KIR2DL8 Patr-KIR2DL8*002 None AC155174, AM279149 Biassoni, unpublished
Patr-KIR2DL8 Patr-KIR2DL8*003 None BX842589 (Sambrook et al. 2005)
Patr-KIR2DL9 Patr-KIR2DL9*001 None AC155174
Patr-KIR2DL9 Patr-KIR2DL9*002 None AM292657 Biassoni, unpublished
Patr-KIR2DL9 Patr-KIR2DL9*003 None AM400233 Biassoni, unpublished
Patr-KIR2DS4 Patr-KIR2DS4*001 None HM068617
Patr-KIR2DS4 Patr-KIR2DS4*002 None AF258807
Patr-KIR3DL1 Patr-KIR3DL1*001:01 None AC155174
Patr-KIR3DL1 Patr-KIR3DL1*001:02 None AF266729 (Rajalingam et al. 2001)
Patr-KIR3DL1 Patr-KIR3DL1*002 None BX842589, AF258798 (Sambrook et al. 2005)
Patr-KIR3DL1 Patr-KIR3DL1*003 None AF266730 (Rajalingam et al. 2001)
Patr-KIR3DL1 Patr-KIR3DL1*004 None AF258799
Patr-KIR3DL1 Patr-KIR3DL1*005 None HM068617
Patr-KIR3DL3 Patr-KIR3DL3*001 None HM068617
Patr-KIR3DL3 Patr-KIR3DL3*002 None BX842589
Patr-KIR3DL3 Patr-KIR3DL3*003 None AC155174
Patr-KIR3DL3 Patr-KIR3DL3*004 None AY327500
Patr-KIR3DL4 Patr-KIR3DL4*001:01 None AM400232 Biassoni, unpublished
Patr-KIR3DL4 Patr-KIR3DL4*001:02 None AF258800 (Khakoo et al. 2000)
Patr-KIR3DL4 Patr-KIR3DL4*002 None HM068617 (Abi-Rached et al. 2010)
Patr-KIR3DL5 Patr-KIR3DL5*001 None AM400235 Biassoni, unpublished
Patr-KIR3DL5 Patr-KIR3DL5*003:01 None AF258801 (Khakoo et al. 2000)
Patr-KIR3DL5 Patr-KIR3DL5*004 None AC155174, AM292659 Biassoni, unpublished
Patr-KIR3DS2 Patr-KIR3DS2*001 None AC155174
Patr-KIR3DS2 Patr-KIR3DS2*002 None AF258803
Patr-KIR3DS6 Patr-KIR3DS6*001 None AM396937 Biassoni, unpublished
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Table 6.

Allele designations and their previous names

Gene Allele designation Previous designations Accession number Reference
Poab-KIR2DL10 Poab-KIR2DL10*001 2DLA AF470358 (Guethlein et al. 2002)
Poab-KIR2DL11 Poab-KIR2DL11*001 2DLB EF014479 (Guethlein et al. 2007b)
Poab-KIR2DL12 Poab-KIR2DL12*001 2DLC AC200148
Poab-KIR2DL5 Poab-KIR2DL5*001 2DL5 AC200148
Poab-KIR2DS10 Poab-KIR2DS10*001 None AF470364 (Guethlein et al. 2002)
Poab-KIR2DS13 Poab-KIR2DS13*001 2DSC1/2DSB AF470362 (Guethlein et al. 2002)
Poab-KIR2DS14 Poab-KIR2DS14*001 2DSB/2DSD2 AF470361 (Guethlein et al. 2002)
Poab-KIR2DS14 Poab-KIR2DS14*002 2DSA/2DSD1 AF470360 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*001:01 3DLH AF470373 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*001:02 None AC200148
Poab-KIR3DL1 Poab-KIR3DL1*002 3DLC AF470367 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*003 None AF470372 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*004:01 3DLD2 AF470369 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*004:02 3DLD1 EF014479 (Guethlein et al. 2007b)
Poab-KIR3DL1 Poab-KIR3DL1*005 3DLA AF470365 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*006 3DLI AF470374 (Guethlein et al. 2002)
Poab-KIR3DL1 Poab-KIR3DL1*007 3DLB AF470366 (Guethlein et al. 2002)
Poab-KIR3DL3 Poab-KIR3DL3*001 3DL3 AC200148
Poab-KIR3DS1 Poab-KIR3DS1*001 3DS1 AF470375 (Guethlein et al. 2002)
Poab-KIRDP Poab-KIRDP*001 DP AC200148
Popy-KIR2DS10 Popy-KIR2DS10*001 2DSD/2DSA AF470364 (Guethlein et al. 2002)
Popy-KIR2DS13 Popy-KIR2DS13*001 2DSC2/2DSB AF470363 (Guethlein et al. 2002)
Popy-KIR3DL1 Popy-KIR3DL1*001 3DLF AF470372 (Guethlein et al. 2002)
Popy-KIR3DL1 Popy-KIR3DL1*002:01 3DLE2 AF470371 (Guethlein et al. 2002)
Popy-KIR3DL1 Popy-KIR3DL1*002:02 3DLE1 AF470370 (Guethlein et al. 2002)
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Table 7.

Allele designations and their previous names

Gene Allele designation Previous designations Accession number Breed Reference
Bota-KIR2DL1 Bota-KIR2DL1*001 KIR2DL1 AY075102,AF490399 UnknownHolstein (McQueen et al. 2002; Storset et al. 2003; Zimin et al. 2009)
Bota-KIR2DL1 Bota-KIR2DL1*002 None JX848327 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR2DS1 Bota-KIR2DS1*001N KIR2DS1 JX848328 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR2DS2 Bota-KIR2DS2*001N None JX848329 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR2DS3 Bota-KIR2DS3*001N None JX848330 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR2DXS1 Bota-KIR2DXS1*001 None AF490400 Holstein (Storset et al. 2003)
Bota-KIR2DXP1 Bota-KIR2DXP1*001 None JX848331 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR2DXP2 Bota-KIR2DXP2*001 None JX848332 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXL1 Bota-KIR3DXL1*001 KIR3DL1 AF490402 Holstein (Storset et al. 2003; Zimin et al. 2009)
Bota-KIR3DXL1 Bota-KIR3DXL1*002 None JX848333 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXL2 Bota-KIR3DXL2*001 None JX848334 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXL3 Bota-KIR3DXL3*001 None JX848335 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXL4 Bota-KIR3DXL4*001 KIR3DL2–001 EF197118 Holstein-Freisian (Dobromylskyj and Ellis 2007; Zimin et al. 2009)
Bota-KIR3DXL4 Bota-KIR3DXL4*002 None JX848336 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXL5 Bota-KIR3DXL5*001 None JX848337 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXL6 Bota-KIR3DXL6*001N KIR3DL1P AY075103JX848338 UnknownHolstein-Freisian (McQueen et al. 2002) (Sanderson et al. 2014)
Bota-KIR3DXL6 Bota-KIR3DXL6*002 KIR3DL3 EF197119 Holstein-Freisian (Dobromylskyj and Ellis 2007; Zimin et al. 2009)
Bota-KIR3DXL7 Bota-KIR3DXL7*001 None JX848339 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXS1 Bota-KIR3DXS1*001 KIR3DS1 AF490401 Holstein (Storset et al. 2003; Zimin et al. 2009)
Bota-KIR3DXS1 Bota-KIR3DXS1*002 KIR3DS1–002 EF197120 Holstein-Freisian (Dobromylskyj and Ellis 2007)
Bota-KIR3DXS1 Bota-KIR3DXS1*003 None JX848340 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXS2 Bota-KIR3DXS2*001N None JX848341 Holstein-Freisian (Sanderson et al. 2014)
Bota-KIR3DXS3 Bota-KIR3DXS3*001N None JX848342 Holstein-Freisian (Sanderson et al. 2014)
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Each KIR allele name includes a unique number corresponding to up to three sets of digits separated by colons. All alleles are given a three-digit name, which corresponds to the first set of digits; longer names are assigned only when necessary.

The digits placed before the first colon describe the alleles that differ at non-synonymous substitutions (also called coding substitutions). Alleles that differ only by synonymous nucleotide substitutions (also called silent or non-coding substitutions) but are within the coding sequence are distinguished by their second sets of digits. Alleles that only differ by sequence polymorphisms in the introns, or in the 5′ or 3′ untranslated regions that flank the exons and introns, are distinguished by their third sets of digits.

In addition to the unique allele number, optional suffixes can be added to an allele name to indicate the expression status of the gene and/or its encoded protein. Alleles known not to be expressed—so called “Null” alleles—have been given the suffix “N.” Alleles that have been shown to be alternatively expressed may have the suffix “L,” “S,” “C,” “A,” or “Q.”

The suffix “L” is used to indicate an allele that has been shown to have “Low” cell surface expression when compared to normal levels. The “S” suffix is used to denote an allele specifying a protein which is expressed as a soluble, “Secreted” molecule and is not present on the cell surface. The “C” suffix is assigned to alleles producing proteins that are present in the “Cytoplasm” and not on the cell surface. An “A” suffix indicates an “Aberrant” expression, where there is doubt as to whether a protein is actually expressed. A “Q” suffix is used when the expression of an allele is “Questionable,” given that the mutation seen in the allele has been shown to affect normal expression levels in other alleles and other KIR genes.

As of May 2018, no alleles have been named with the “C,” “A,” “Q,” or “S” suffixes.

A schematic representation of the syntax for the non-human KIR allele designation is shown in Fig. 1.

Fig. 1. Non-human KIR nomenclature.

Fig. 1

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Details the syntax and structure of a non-human KIR allele designation

Species-specific guidelines

Naming rhesus macaque KIR genes

The Mamu-KIR sequences fall into a number of distinct lineages based on phylogenetic analysis. Most sequences correspond to lineage II KIR and are further divided into those encoding KIR that have long cytoplamic tails or short cytoplasmic tails. The genes have been numbered sequentially and where possible the gene name has the same the same number as the first reported allele for that gene. For example, the Mamu-KIR3DL1 gene (Hershberger et al. 2001) was renamed Mamu-KIR3DL01*001.

The nomenclature uses a two-digit numbering of individual genes for the macaque sequences as seen with the naming of Mamu-KIR3DL01*001. This renaming aims to avoid confusion with previous sequence names. Subsequent analysis has shown that some of the proposed sequences of different genes are actually allelic variants of the same gene. Rather than skipping numbers to avoid confusion, it was thought better to introduce the two-digit numbering system.

Recombinant alleles are named according to the locus, which provide the majority of the sequence. For example, the sequence originally named Mamu-KIR3DL5 (Hershberger et al. 2001) is a recombinant of Mamu-KIR3DL01 and Mamu-KIR3DL07. As such, it has been renamed as an allele of Mamu-KIR3DL01, Mamu-KIR3DL01*005. This principal has also been applied to recombinant alleles in other species.

Along with the lineage II KIR genes, rhesus macaques have KIR genes for lineage I, III, and V KIR. The lineage I KIR gene in rhesus macaques is orthologous to other primate lineage 1 KIR, referred to as 2DL4 and has been named Mamu-KIR2DL04. A single lineage III KIR is also present on some Mamu-KIR haplotypes and in all cases appears to be expressed as a one Ig domain KIR. It has been named Mamu-KIR1D. Finally, there is a lineage V KIR gene that is expressed as either a two Ig or three Ig domain KIR. The published genomic sequence shows the gene to contain three Ig domain encoding exons; however, due to splicing out of exon 4, also two Ig domain KIR variants are expressed. The majority of the rhesus macaque gene sequence appears orthologous to hominoid KIR3DL3 sequences, the exception being exon 3 [encoding the D0 domain] which appears more like the hominoid KIR2DL5 sequences. This sequence relationship coupled with the presence of splice variants that lacked exon 4 led to the naming of some of these sequences as Mamu-KIR2DL5. The presence of the intact gene as evidenced by the published genomic sequence, as well as the existence of full-length [three Ig domain containing] sequences has led us to propose naming this gene as Mamu-KIR3DL20. This distinguishes this gene from the remaining Mamu-KIR3DL as well as retaining the name of one of the first mRNA sequences that included all three Ig domain encoding exons, see Table 1 for further details. A full list of Mamu-KIR sequences is described in Table 4.

The identification of sequences in other Macaque species will follow the same rules, and use the species prefix (Mafa-KIR, Mane-KIR), and that genes would be named to match the closest rhesus gene.

Naming chimpanzee KIR genes

Three studies (Abi-Rached et al. 2010; Khakoo et al. 2000; Sambrook et al. 2005) have described complete sequences of three chimpanzee haplotypes. In addition, the analysis of chimpanzee KIR genotypes has inferred the organization of genes infers the existence of another 17 chimpanzee KIR haplotypes. These analyses have defined 13 different Patr-KIR genes.

In all chimpanzee KIR haplotypes, the framework gene at the telomeric end is a lineage II KIR gene. Formerly, two variants, now known to occupy this position, were named Pt-KIR3DL1/2 and Pt-KIR3DL3. The name Pt-KIR3DL1/2 was given to reflect its close relationship to both human KIR3DL1 and KIR3DL2. Although segregation analysis showed that Pt-KIR3DL3 and KIR3DL1/2 were never present on the same haplotype, Pt-KIR3DL3 was given a different name because it has a distinctive sequence. We are renaming the Pt-KIRDl1/2 and Pt-KIR3DL3 as allelic variants of Patr-KIR3DL1, the new name for the framework gene at the telomeric end of the chimpanzee KIR locus. This will allow the Patr-KIR3DL3 name to be given to the gene previously known as Patr-KIRC1, and which is orthologous to human KIR3DL3, the framework gene at the centromeric end of the KIR locus. See Table 2 for further details. A full list of Patr-KIR sequences is described in Table 5.

Naming orangutan KIR genes

In the initial description of orangutan KIR cDNA (Guethlein et al. 2002), the sequences were given letter designations because their relationships, either alleles or genes, were uncertain. Subsequent studies (Guethlein et al. 2007a; Guethlein et al. 2017; Locke et al. 2011; Mager et al. 2001) have provided complete sequences of three orangutan KIR haplotypes, as well as genotyping data that has allowed the structures of two additional KIR haplotypes to be inferred. These genomic data, in combination with the cDNA sequences, defined 11 KIR genes and 1 KIR pseudogene in the orangutan. At first, all orangutan KIR were named as “Popy” (Guethlein et al. 2007b). The orangutan KIR is now divided into two series corresponding to the two species of orangutan: Popy for Pongo pygmaeus and Poab for Pongo abelii depending on species of origin. Some KIR alleles are present in both orangutan species. These alleles shared have been given a different name in each species (Guethlein et al. 2017; Guethlein et al. 2015), see Table 3: for further details. A full list of Popy-KIR and Poab-KIR sequences is given in Table 6.

Naming cattle KIR genes

Assembly of the first cattle KIR haplotype allowed previously known cDNA sequences to be assigned to particular genes and allelic relationships to be defined (Dobromylskyj and Ellis 2007; Guethlein et al. 2007a; Hammond et al. 2016; Mager et al. 2001; Sanderson et al. 2014). This presents the opportunity to adopt an accurate and logical nomenclature system. Cattle KIR cDNA sequences were previously named using the established convention of Ig domain number and tail length. However, these alleles were annotated prior to the discovery of a second deeply divergent KIR lineage, the KIR3DX lineage (Guethlein et al. 2007a). The majority of the expanded cattle KIR belong to this second lineage. In developing a nomenclature system for the cattle KIR, we have incorporate their lineage ancestry within the name. Cattle KIR have been prefixed with a four-letter species designation “Bota” (Bos taurus) in line with non-human primates. Where possible previously named Bota-KIR has retained the same name with only the addition of an “X” after the domain number if from the KIR3DX lineage. There are three exceptions; Bota-KIR3DL1P and Bota-KIR3DL3, which are allelic, and Bota-KIR3DL2. These previously described cDNA sequences are all members of the KIR3DX lineage. Based on their position in the cattle haplotype and their relationships to other genes, Bota-KIR3DL1P was renamed Bota-KIR3DXL6*001N, Bota-KIR3DL3 was renamed Bota-KIR3DXL6*002, and Bota-KIR3DL2 was renamed Bota-KIR3DXL4. We have identified 16 cattle KIR genes. The proposed nomenclature for cattle KIR is given in Table 7.

Future guidelines

The sequences described in this report will be included in the Immuno Polymorphism Database (IPD) (Robinson et al. 2013). They will be maintained as a component of the IPD and be accessible at https://www.ebi.ac.uk/ipd/nhkir/. New sequences for any of the above species can be submitted using the current submission tool. As with the other databases, there are requirements that should be met before formal names can be given and the submitted KIR are included in the database. First, submission of full-length sequences is encouraged and for some species like rhesus macaque is already mandatory. Second, novel sequences must be confirmed, either through their replication in multiple individuals or at a minimum by coming from multiple independent PCR/cloning experiments. Full guidelines for submission of non-human KIR sequences to IPD can be found at https://www.ebi.ac.uk/ipd/nhkir/submission/help.

As KIR sequence data from other species reaches the level of the species included in this report, those species can be included in the database. The inclusion of a species will be at the discretion of the Nomenclature Committee and IPD and will be based on the number of sequences available as well as evidence of identified genes and haplotype structure.

Funding

JAH and NDS were supported by the United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) through projects BBS/E/I/00001410 and BBS/E/I/00001710.

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